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Home , A4GALT, Acetylesterase, ACTG2, Acylphosphatase, ADAM11, ADAM23

Supplementary material J Neurol Neurosurg Psychiatry

Gene names IDs Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] IGLC7 A0M8Q6 4 1 55,7 11,303 Ig lambda-7 chain C region SSC5D A1L4H1;A1L4H1-2 15 15 15,4 165,74 Soluble scavenger receptor cysteine- rich domain-containing protein SSC5D KIAA1467 A2RU67 2 2 5,3 67,038 Uncharacterized protein KIAA1467 MEGF11 A6BM72- 2 2 4,1 101,55 Multiple epidermal -like 2;A6BM72;A6BM72- domains protein 11 4;A6BM72-3 PGP A6NDG6 1 1 5,9 34,006 Phosphoglycolate BTBD17 A6NE02 1 1 4,4 52,47 BTB/POZ domain-containing protein 17 IGLON5 A6NGN9 6 6 24,1 36,794 IgLON family member 5 RAP1B;RAP1A P61224-4;P61224- 2 2 19 16,033 Ras-related protein Rap-1b;Ras-related 3;P61224;A6NIZ1;P612 protein Rap-1b-like protein;Ras- 24-2;P62834 related protein Rap-1A IGHV1OR21-1 A6NJS3 1 1 12,5 13,37 Putative V-set and immunoglobulin domain-containing-like protein IGHV1OR21-1 SHISA7 A6NL88 1 1 2,4 56,213 Protein shisa-7 VSTM2B A6NLU5 6 6 27,4 30,297 V-set and transmembrane domain- containing protein 2B OR2AG1;OR2AG2 Q9H205;A6NM03 1 1 2,2 35,27 2AG1;Olfactory receptor 2AG2 LRRC53 A6NM62 2 2 2,7 140,74 Leucine-rich repeat-containing protein 53 IGLL5;IGLC1 B9A064;P0CG04 9 4 46,7 23,063 Immunoglobulin lambda-like polypeptide 5;Ig lambda-1 chain C regions PRR24 C9JVW0 1 1 17,6 14,668 -rich protein 24

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ALB CON__P02768- 121 113 93,9 69,366 Serum albumin 1;P02768;P02768- 2;P02768-3 CCER2 I3L3R5 5 5 15,4 30,351 Coiled-coil domain-containing glutamate-rich protein 2 DNASE2 O00115-2;O00115 2 2 8,5 33,615 -2-alpha ACOT7 O00154-6;O00154- 1 1 4,9 36,567 Cytosolic acyl coenzyme A thioester 4;O00154-5;O00154- 7;O00154

MASP2 O00187;O00187-2 3 3 6,6 75,702 Mannan-binding 2;Mannan-binding lectin 2 A chain;Mannan-binding lectin serine protease 2 B chain SIRPB1 O00241 3 1 8,8 43,211 Signal-regulatory protein beta-1 ATOX1 O00244 4 4 64,7 7,4016 Copper transport protein ATOX1 PGRMC1 O00264;O00264- 5 5 35,4 21,671 Membrane-associated progesterone 2;O15173;O15173-2 receptor component 1

LEFTY2 O00292-2;O00292 2 2 8,7 37,092 Left-right determination factor 2 CLIC1 O00299 11 11 70,1 26,922 Chloride intracellular channel protein 1 MATN2 O00339- 11 11 17,2 104,77 Matrilin-2 2;O00339;O00339- 3;O00339-4 QSOX1 O00391;O00391-2 21 21 36,3 82,577 Sulfhydryl oxidase 1 GFRA2 O00451;O00451- 10 10 30,4 51,543 GDNF family receptor alpha-2 3;O00451-2 GOLIM4 O00461 9 9 20,3 81,879 Golgi integral 4 MANBA O00462 23 23 30,5 100,89 Beta-mannosidase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] AGRN O00468-6;O00468- 39 39 31,3 214,84 ;Agrin N-terminal 110 kDa 3;O00468-5;O00468- subunit;Agrin C-terminal 110 kDa 4;O00468- subunit;Agrin C-terminal 90 kDa 7;O00468;O00468-2 fragment;Agrin C-terminal 22 kDa fragment

BIN1 O00499-9;O00499- 4 4 17,6 45,563 Myc box-dependent-interacting 10;O00499-7;O00499- protein 1 8;O00499-4;O00499- 6;O00499-11;O00499- 3;O00499-2;O00499- 5;O00499

CHL1 O00533 42 1 44,8 135,07 Neural molecule -like protein;Processed neural L1-like protein DLL1 O00548 2 2 5,3 78,055 Delta-like protein 1 SDCBP O00560;O00560- 4 4 24,5 32,444 Syntenin-1 3;O00560-2 RNASET2 O00584;O00584-2 14 14 53,9 29,48 T2 PODXL O00592-2;O00592 1 1 2,5 55,385 Podocalyxin CYR61 O00622 1 1 3,7 42,026 Protein CYR61 MAN2B1 O00754-2;O00754 10 10 12,2 113,61 Lysosomal alpha- mannosidase;Lysosomal alpha- mannosidase A ;Lysosomal alpha-mannosidase B peptide;Lysosomal alpha-mannosidase C peptide;Lysosomal alpha- mannosidase D peptide;Lysosomal alpha-mannosidase E peptide

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ISLR O14498 11 11 52,3 45,997 Immunoglobulin superfamily containing leucine-rich repeat protein BAI1 O14514 10 10 10,9 173,5 Brain-specific angiogenesis inhibitor 1 PTPRT O14522;O14522-1 8 8 7,4 162,13 Receptor-type - T ASTN1 O14525- 6 6 7,5 143,98 Astrotactin-1 2;O14525;O14525-3

NCAN O14594 23 22 23,5 143,09 core protein PRRG1 O14668-2;O14668 2 2 15,9 9,4607 Transmembrane gamma- carboxyglutamic acid protein 1 ADAM10 O14672;O14672-2 12 12 22,9 84,141 and domain-containing protein 10 SLC9A3R1 O14745;O14745-2 2 2 6,4 38,868 Na(+)/H(+) exchange regulatory NHE-RF1 TPP1 O14773;O14773-2 11 11 29 61,247 Tripeptidyl-peptidase 1 NRP1 O14786-3;O14786- 14 14 38,1 68,375 -1 2;O14786 APOL1 O14791- 8 8 19,2 42,158 L1 3;O14791;O14791-2

MSTN O14793 5 4 18,9 42,75 Growth/differentiation factor 8 CPLX1 O14810 1 1 14,9 15,03 Complexin-1 PSMA7;PSMA8 O14818;O14818- 4 4 19,8 27,887 Proteasome subunit alpha type- 2;O14818-4;Q8TAA3- 7;Proteasome subunit alpha type-7- 2;Q8TAA3-5;Q8TAA3 like

GIPC1 O14908-2;O14908 1 1 6,4 26,071 PDZ domain-containing protein GIPC1 PCDH17 O14917-2;O14917 16 16 29,8 96,568 -17

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LECT2 O14960 2 2 21,2 16,39 Leukocyte cell-derived chemotaxin-2 PLXNB2 O15031 36 36 29,8 205,12 Plexin-B2 SEMA3E O15041-2;O15041 6 6 10,2 82,423 Semaphorin-3E ADAMTS3 O15072 2 2 2,3 135,6 A disintegrin and metalloproteinase with motifs 3 DCLK1 O15075-2;O15075 1 1 1,5 81,099 Serine/-protein DCLK1 NPC1 O15118 3 3 2,7 142,17 Niemann-Pick C1 protein SCAMP1 O15126-2;O15126 1 1 7 18,042 Secretory carrier-associated membrane protein 1 ARPC1B O15143 1 1 3,5 40,949 -related protein 2/3 complex subunit 1B EPHB6 O15197- 8 8 29,6 57,497 type-B receptor 6 3;O15197;O15197-2

ADAMDEC1 O15204-2;O15204 2 2 8,2 43,556 ADAM DEC1 LAMA5 O15230;O15230-2 28 28 11,6 399,73 subunit alpha-5 MATN3 O15232-2;O15232 4 4 14,4 48,316 Matrilin-3 VGF O15240 26 26 55 67,257 Neurosecretory protein VGF;Neuroendocrine regulatory peptide-1;Neuroendocrine regulatory peptide-2;Antimicrobial peptide VGF[554-577] CHAD O15335 8 8 33,4 40,475 Chondroadherin GPR37 O15354 4 4 8,3 67,113 Prosaposin receptor GPR37 NCAM2 O15394;O15394-2 30 30 47,6 93,045 Neural cell adhesion molecule 2 STX7 O15400-2;O15400 3 3 17,6 27,4 -7 ST8SIA5 O15466;O15466-2 4 4 14,4 43,894 Alpha-2,8- 8E FABP7 O15540;O15540-2 2 2 25 14,889 -binding protein, brain FLRT2 O43155 2 2 2,9 74,048 Leucine-rich repeat transmembrane protein FLRT2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PLXNB1 O43157- 13 13 13,3 214,41 Plexin-B1 2;O43157;O43157-3

ST8SIA3 O43173 8 8 22,9 43,969 Sia-alpha-2,3-Gal-beta-1,4-GlcNAc- R:alpha 2,8-sialyltransferase DYNC1LI2 O43237-2;O43237 2 2 7 45,004 Cytoplasmic 1 intermediate chain 2 KLK10 O43240 2 2 10,1 30,17 -10 SPINT1 O43278-2;O43278 7 7 14,2 56,885 Kunitz-type protease inhibitor 1 SPINT2 O43291;O43291-2 2 2 8,7 28,228 Kunitz-type protease inhibitor 2 LRRTM2 O43300 3 3 7 59,076 Leucine-rich repeat transmembrane neuronal protein 2 TXNL1 O43396 4 4 23,2 32,251 Thioredoxin-like protein 1 TPD52L2 O43399-6;O43399- 2 2 18,4 17,473 Tumor protein D54 2;O43399- 4;O43399;O43399- 3;O43399-5;O43399-7

COCH O43405;O43405-2 10 10 23,3 59,482 Cochlin GRID2 O43424-2;O43424 1 1 1,2 102,82 ionotropic, delta-2 EPB41L2 O43491- 6 6 9,3 95,541 Band 4.1-like protein 2 4;O43491;O43491- 3;O43491-2 TGOLN2 O43493-2;O43493- 9 9 25,2 45,879 Trans-Golgi network integral 5;O43493- membrane protein 2 3;O43493;O43493- 4;O43493-6 LAMTOR5 O43504 2 2 44 9,6138 Ragulator complex protein LAMTOR5 B3GNT1 O43505 20 20 60,2 47,119 N-acetyllactosaminide beta-1,3-N- acetylglucosaminyltransferase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TNFSF12;TNFSF13 O43508-2;O75888- 3 2 12,1 36,588 5;O75888- superfamily member 12;Tumor 4;O75888;O75888- necrosis factor ligand superfamily 2;O75888-3 member 12, membrane form;Tumor necrosis factor ligand superfamily member 12, secreted form;Tumor necrosis factor ligand superfamily member 13 CHST10 O43529 7 7 18,8 42,206 Carbohydrate sulfotransferase 10 SGCE O43556;O43556- 11 11 35,7 49,85 Epsilon-sarcoglycan 3;O43556-4 RNF13 O43567;O43567-2 6 6 15,2 42,813 E3 ubiquitin-protein RNF13 ITM2A O43736-2;O43736 2 2 8,7 24,993 Integral membrane protein 2A ANGPTL7 O43827 5 5 19,4 40,018 -related protein 7 CALU O43852-10;O43852- 5 5 22,3 26,326 Calumenin 6;O43852;O43852- 3;O43852-13;O43852- 14;O43852-9;O43852- 11;O43852-8;O43852- 5;O43852-2;O43852- 4;O43852-12;O43852- 7;O43852-15

EDIL3 O43854-2;O43854 4 4 13,6 52,747 EGF-like repeat and discoidin I-like domain-containing protein 3 CD5L O43866 8 8 34 38,087 CD5 antigen-like

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TLL1 O43897-2;O43897 2 2 3,3 44,185 Tolloid-like protein 1 EXTL3 O43909 5 5 7,1 104,75 Exostosin-like 3 CHST1 O43916 3 3 15,1 46,714 Carbohydrate sulfotransferase 1 BAI2 O60241-4;O60241- 5 5 5,4 169,2 Brain-specific angiogenesis inhibitor 2 3;O60241-2;O60241

BAI3 O60242 4 4 2,7 171,52 Brain-specific angiogenesis inhibitor 3 HS6ST1 O60243-2;O60243 3 3 13,7 29,87 Heparan-sulfate 6-O-sulfotransferase 1 PCDH7 O60245;O60245-2 11 11 14 116,07 Protocadherin-7 SUSD5 O60279 14 14 29,3 68,02 Sushi domain-containing protein 5 MGRN1 O60291- 2 2 7,9 58,304 E3 ubiquitin-protein ligase MGRN1 4;O60291;O60291- 3;O60291-2 PCDHGA12;PCDHGA5;PC O60330;O60330- 6 3 7,2 100,95 Protocadherin gamma- DHGA4;PCDHGA7;PCDH 2;Q9Y5G8;Q9Y5G8- A12;Protocadherin gamma- GA8 2;Q9Y5G9;Q9Y5G6;Q9Y A5;Protocadherin gamma- 5G5;Q9Y5G6- A4;Protocadherin gamma- 2;Q9Y5G9-2;Q9Y5G5- A7;Protocadherin gamma-A8 2;Q9Y5G1;Q9Y5H4;Q9Y 5G1-2;Q9Y5H4-2

LY75 O60449-3;O60449- 11 11 7,8 209,44 Lymphocyte antigen 75 2;O60449;Q8IX05 NRP2 O60462-3;O60462- 18 18 29,5 104,28 Neuropilin-2 4;O60462-5;O60462- 2;O60462;O60462-6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MAN1A2 O60476 8 7 11,7 73,003 Mannosyl-oligosaccharide 1,2-alpha- mannosidase IB BRINP1 O60477;O60477- 4 4 5,7 88,76 BMP/retinoic acid-inducible neural- 2;O60477-3 specific protein 1 PLXNC1 O60486 4 4 4,1 175,74 Plexin-C1 STX10 O60499-2;O60499 1 1 5,5 22,445 Syntaxin-10 MGEA5 O60502-3;O60502- 1 1 2,1 76,192 Bifunctional protein NCOAT;Protein O- 2;O60502-4;O60502 GlcNAcase;Histone acetyltransferase

TPST1 O60507 5 5 20 42,188 Protein-tyrosine sulfotransferase 1 PLOD3 O60568 10 10 15,6 84,784 Procollagen-,2-oxoglutarate 5- dioxygenase 3 GFRA3 O60609;O60609-2 4 4 12,2 44,51 GDNF family receptor alpha-3 Sep 15 O60613;O60613-2 4 4 30,9 17,79 15 kDa selenoprotein PLIN3 O60664-4;O60664- 2 2 7,8 45,803 Perilipin-3 3;O60664;O60664-2

TOM1 O60784-3;O60784- 2 2 5,8 48,672 Target of Myb protein 1 4;O60784;O60784-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HIST1H2BL;HIST1H2BM; Q99880;Q99879;Q9987 1 1 7,1 13,952 Histone H2B type 1-L;Histone H2B type HIST1H2BN;HIST1H2BH; 7;Q93079;Q8N257;Q5 1-M;Histone H2B type 1-N;Histone HIST3H2BB;HIST2H2BF;H QNW6;Q16778;P62807 H2B type 1-H;Histone H2B type 3- IST2H2BE;HIST1H2BC;HIS ;P58876;P57053;P3377 B;Histone H2B type 2-F;Histone H2B T1H2BD;H2BFS;HIST1H2 8;P23527;P06899;O608 type 2-E;Histone H2B type 1- BB;HIST1H2BO;HIST1H2B 14;Q96A08;Q5QNW6-2 C/E/F/G/I;Histone H2B type 1- J;HIST1H2BK;HIST1H2BA D;Histone H2B type F-S;Histone H2B type 1-B;Histone H2B type 1-O;Histone H2B type 1-J;Histone H2B type 1- K;Histone H2B type 1-A

GPR37L1 O60883 2 2 5,4 52,77 Prosaposin receptor GPR37L1 CUTA O60888- 7 7 61,5 16,832 Protein CutA 3;O60888;O60888-2

SCN2B O60939 3 3 19,5 24,326 channel subunit beta-2 FCGR3B O75015 2 1 11,6 26,216 Low affinity immunoglobulin gamma Fc region receptor III-B PLXNA2 O75051;O75051-2 7 7 5,9 211,1 Plexin-A2 SDC3 O75056 1 1 5 45,496 Syndecan-3 FAM20B O75063 7 7 25,4 46,432 Glycosaminoglycan xylosylkinase EFCAB14 O75071 4 4 12,5 55,031 EF-hand calcium-binding domain- containing protein 14 ADAM23 O75077-3;O75077- 7 7 14,8 92,129 Disintegrin and metalloproteinase 2;O75077 domain-containing protein 23

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ADAM11 O75078;O75078-2 12 12 26,7 83,418 Disintegrin and metalloproteinase domain-containing protein 11 WDR1 O75083;O75083-3 9 9 21,1 66,193 WD repeat-containing protein 1 SLIT1 O75093;O75093-2 4 4 3,6 167,92 Slit homolog 1 protein SLIT3 O75094- 6 6 5,9 156,76 Slit homolog 3 protein 2;O75094;O75094- 3;O75094-4 MEGF6 O75095-2;O75095 1 1 2 128,61 Multiple -like domains protein 6 LRP4 O75096 3 3 2,3 212,04 Low-density receptor- related protein 4 ASTN2 O75129-2;O75129- 5 5 6,4 142,54 Astrotactin-2 3;O75129;O75129- 6;O75129-4 ICOSLG O75144;O75144- 6 6 25,2 33,348 ICOS ligand 2;O75144-3 ADAMTS4 O75173;O75173-2 4 4 6,8 90,196 A disintegrin and metalloproteinase with thrombospondin motifs 4 GGCT O75223;O75223- 4 4 20,7 21,007 Gamma-glutamylcyclotransferase 3;O75223-2;O75223-4

SEMA7A O75326;O75326-2 24 24 38,9 74,823 Semaphorin-7A CILP O75339 2 2 2,3 132,56 intermediate layer protein 1;Cartilage intermediate layer protein 1 C1;Cartilage intermediate layer protein 1 C2 TBCA O75347;O75347-2 4 4 34,3 12,855 -specific A ENTPD6 O75354-2;O75354- 7 7 17,1 51,158 Ectonucleoside triphosphate 3;O75354 diphosphohydrolase 6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] BCAS1 O75363;O75363-2 1 1 2,6 61,708 Breast carcinoma-amplified sequence 1 SH3BGRL O75368 9 9 85,1 12,774 SH3 domain-binding glutamic acid- rich-like protein GPC4 O75487-2;O75487 5 4 16,3 54,91 -4;Secreted glypican-4 CA11 O75493 4 4 14,9 36,238 -related protein 11 CLN5 O75503 9 9 29,1 41,496 Ceroid-lipofuscinosis neuronal protein 5 TNFRSF21 O75509 9 9 14,8 71,844 Tumor necrosis factor receptor superfamily member 21 LRP6 O75581 2 2 1,4 180,43 Low-density lipoprotein receptor- related protein 6 PGLYRP1 O75594 1 1 8,2 21,731 recognition protein 1 CREG1 O75629 2 2 19,5 24,074 Protein CREG1 FCN3 O75636-2;O75636 1 1 4,9 31,677 Ficolin-3 SCRG1 O75711 5 5 68,4 11,081 Scrapie-responsive protein 1 B3GALNT1 O75752 12 12 45,6 39,511 UDP-GalNAc:beta-1,3-N- acetylgalactosaminyltransferase 1 PALM O75781-2;O75781 4 4 14 37,157 Paralemmin-1 ATP6AP2 O75787-2;O75787 10 10 42,1 35,612 receptor PSMD10 O75832 1 1 11,9 24,428 26S proteasome non-ATPase regulatory subunit 10 IDH1 O75874 6 6 17,1 46,659 [NADP] cytoplasmic ATRN O75882-3;O75882- 25 25 26,6 133,7 Attractin 2;O75882 C1QL1 O75973 3 2 15,1 26,452 C1q-related factor CPD O75976;O75976-2 10 10 9 152,93 D STC2 O76061 2 2 7,9 33,248 Stanniocalcin-2 SNCG O76070 6 6 52,8 13,331 Gamma-synuclein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] WISP2 O76076-2;O76076 2 2 20,2 22,577 WNT1-inducible-signaling pathway protein 2 DDAH1 O94760;O94760-2 13 12 57,2 31,121 N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 B3GAT3 O94766-2;O94766 5 5 28,9 34,624 Galactosylgalactosylxylosylprotein 3- beta- 3 ECM2 O94769;Q8N3V7-2 22 3 41,3 79,788 protein 2 ECM2 O94769-2 21 2 41,2 73,347 Extracellular matrix protein 2 LY6H O94772;O94772-2 5 5 35 14,669 Lymphocyte antigen 6H CNTN5 O94779-4;O94779- 12 12 20,6 100,33 Contactin-5 2;O94779 SLIT2 O94813-3;O94813- 2 2 1,7 168,89 Slit homolog 2 protein;Slit homolog 2 2;O94813 protein N-;Slit homolog 2 -product NFASC O94856-6;O94856- 34 3 35,4 137,53 Neurofascin 13;O94856;O94856- 11;O94856-7;O94856- 5;O94856-10;O94856- 3;O94856-8;O94856-2

NFASC O94856-9;O94856- 33 2 33,5 137,61 Neurofascin 4;O94856-12

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SORBS2 O94875-9;O94875- 1 1 3,3 71,685 Sorbin and SH3 domain-containing 5;O94875-3;O94875- protein 2 8;O94875-2;O94875- 4;O94875-12;O94875- 10;O94875- 7;O94875;O94875-11

LRIG2 O94898;Q6UXM1- 7 7 7,6 118,96 Leucine-rich repeats and 2;Q6UXM1 immunoglobulin-like domains protein 2 LPHN1 O94910 21 2 18,5 162,71 -1 LPHN1 O94910-2 20 1 18,4 162,12 Latrophilin-1 ENDOD1 O94919 14 14 41,8 55,016 domain-containing 1 protein GLCE O94923 2 2 4,9 70,1 D-glucuronyl C5-epimerase SLITRK3 O94933 6 6 8,3 108,93 SLIT and NTRK-like protein 3 AP2A2 O94973;O94973- 2 2 2,3 103,96 AP-2 complex subunit alpha-2 2;O94973-3 SEC31A O94979-7;O94979- 2 2 3,1 105,75 Protein transport protein Sec31A 6;O94979-3;O94979- 10;O94979-4;O94979- 9;O94979- 2;O94979;O94979-8

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CLSTN1 O94985 38 2 39,8 109,79 Calsyntenin-1;Soluble Alc-alpha;CTF1- alpha CLSTN1 O94985-2 37 1 39,1 108,64 Calsyntenin-1;Soluble Alc-alpha;CTF1- alpha SLITRK5 O94991;O94991-2 11 9 10,6 107,48 SLIT and NTRK-like protein 5 SEMA3D O95025 3 3 4,6 89,65 Semaphorin-3D PRSS23 O95084;O95084-2 5 5 18,3 43,001 Serine protease 23 NXPH2 O95156 2 1 8,7 29,937 Neurexophilin-2 NXPH3 O95157 1 1 6 28,127 Neurexophilin-3 ZFPL1 O95159 1 1 5,8 34,114 finger protein-like 1 UNC5C O95185-2;O95185 7 7 15,2 66,078 Netrin receptor UNC5C CSPG5 O95196-2;O95196 1 1 2,4 56,982 5 PCDH8 O95206-2;O95206 10 10 14,1 103,63 Protocadherin-8 VAPB O95292-2;O95292 2 1 26,3 11,151 Vesicle-associated membrane protein- associated protein B/C FKBP9;FKBP9P1 O95302- 2 2 7,7 37,046 Peptidyl-prolyl cis-trans 2;O95302;O95302- FKBP9;Putative FK506-binding protein 3;Q75LS8 9-like protein PGLS O95336 7 7 42,2 27,547 6-phosphogluconolactonase GDF11 O95390 6 5 19,9 45,09 Growth/differentiation factor 11 PAPLN O95428;O95428- 21 21 30,4 137,7 Papilin 6;O95428-5;O95428- 4;O95428-2;O95428-3

APOM O95445;O95445-2 8 8 46,3 21,253 Apolipoprotein M ADAMTS2 O95450-2;O95450 4 4 16,1 61,756 A disintegrin and metalloproteinase with thrombospondin motifs 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] H6PD O95479 3 3 5,3 88,892 GDH/6PGL endoplasmic bifunctional protein;Glucose 1-dehydrogenase;6- phosphogluconolactonase LPHN2 O95490-3;O95490- 7 7 9,2 126,16 Latrophilin-2 4;O95490-2;O95490- 5;O95490;O95490- 7;O95490-6

VNN1 O95497;Q9NY84- 3 3 9,7 57,011 Pantetheinase 5;Q9NY84-2;Q9NY84

NPTXR O95502 19 19 45,4 52,846 Neuronal pentraxin receptor FSTL3 O95633-2;O95633 5 5 39,7 24,96 -related protein 3 SEMA4F O95754-2;O95754 2 2 5,4 66,476 Semaphorin-4F AP2A1 O95782-2;O95782 1 1 1,2 105,36 AP-2 complex subunit alpha-1 BAG3 O95817 4 4 7,5 61,594 BAG family molecular chaperone regulator 3 ANGPTL1 O95841 3 3 6,3 56,719 Angiopoietin-related protein 1 BPNT1 O95861- 2 2 8,8 29,188 3(2),5-bisphosphate 1 4;O95861;O95861- 2;O95861-3 DDAH2 O95865 6 5 32,3 29,644 N(G),N(G)-dimethylarginine dimethylaminohydrolase 2 OLFM2 O95897 4 4 11,2 51,386 Noelin-2 ITGBL1 O95965-2;O95965- 4 4 19 38,666 beta-like protein 1 3;O95965 EFEMP2 O95967 11 11 42 49,405 EGF-containing -like extracellular matrix protein 2 RECK O95980 11 11 18,5 106,46 Reversion-inducing cysteine-rich protein with Kazal motifs

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ADH1B;ADH1A P00325;P00325- 2 2 6,9 39,854 1B;Alcohol 2;P07327 dehydrogenase 1A LDHA P00338;P00338- 14 13 48,2 36,688 L- A chain 3;P00338-4;P00338- 5;P00338- 2;Q6ZMR3;P07864 ALDH1A1 P00352;O94788- 10 8 25,3 54,861 Retinal dehydrogenase 1 4;O94788-2;O94788- 3;P47895;P30837;O947 88

GSR P00390-5;P00390- 2 2 5,5 47,267 Glutathione reductase, mitochondrial 4;P00390-2;P00390- 3;P00390 SOD1 P00441 6 6 64,9 15,936 Superoxide dismutase [Cu-Zn] CP P00450 64 57 75,5 122,2 F13A1 P00488 11 11 18,3 83,266 factor XIII A chain PNP P00491 7 7 35,3 32,118 Purine nucleoside HPRT1 P00492;Q9NRG1- 9 9 56,4 24,579 Hypoxanthine-guanine 2;Q9NRG1 phosphoribosyltransferase GOT2 P00505;P00505-2 5 5 14,9 47,517 Aspartate aminotransferase, mitochondrial EGFR P00533;P00533- 11 11 13,3 134,28 Epidermal 4;P00533-3;P00533-2

PGK1 P00558;P00558- 20 20 56,4 44,614 Phosphoglycerate kinase 1 2;P07205 AK1 P00568;Q9Y6K8- 4 4 29,4 21,635 Adenylate kinase isoenzyme 1 2;Q9Y6K8-3;Q9Y6K8

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] F2 P00734;CON__P00735 34 34 60,9 70,036 Prothrombin;Activation peptide fragment 1;Activation peptide fragment 2; light chain;Thrombin heavy chain C1R P00736 29 29 48,4 80,118 Complement C1r subcomponent;Complement C1r subcomponent heavy chain;Complement C1r subcomponent light chain HP P00738;P00738-2 32 15 68,5 45,205 ;Haptoglobin alpha chain;Haptoglobin beta chain HPR P00739;P00739-2 24 7 58,9 39,029 Haptoglobin-related protein F9 P00740;P00740-2 8 8 23,4 51,778 Coagulation factor IX;Coagulation factor IXa light chain;Coagulation factor IXa heavy chain F10 P00742 13 13 25 54,731 Coagulation ;Factor X light chain;Factor X heavy chain;Activated factor Xa heavy chain CFD P00746 9 9 47,4 27,033 Complement PLG P00747;CON__P06868; 52 51 68,4 90,568 Plasminogen; heavy chain Q15195;Q02325 A;Activation peptide;Angiostatin;Plasmin heavy chain A, short form;Plasmin light chain B F12 P00748 13 13 30,2 67,791 Coagulation factor XII;Coagulation factor XIIa heavy chain;Beta-factor XIIa part 1;Beta-factor XIIa part 2;Coagulation factor XIIa light chain CFB P00751;P00751- 43 43 60,9 85,532 ;Complement 2;CON__Q3KUS7 factor B Ba fragment;Complement factor B Bb fragment

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ADA P00813 1 1 8,5 40,764 Adenosine deaminase CA1 P00915 8 8 46,4 28,87 Carbonic anhydrase 1 CA2 P00918 10 10 51,5 29,246 Carbonic anhydrase 2 SERPINC1 P01008;CON__P41361 35 35 60,8 52,602 -III

SERPINA1 P01009;P01009- 50 50 83,3 46,736 Alpha-1-antitrypsin;Short peptide from 2;P01009-3;P20848 AAT SERPINA3 P01011;P01011- 33 33 70,7 47,65 Alpha-1-antichymotrypsin;Alpha-1- 2;P01011-3 antichymotrypsin His-Pro-less AGT P01019 24 24 52,4 53,154 Angiotensinogen;- 1;Angiotensin-2;Angiotensin- 3;Angiotensin-4;Angiotensin 1- 9;Angiotensin 1-7;Angiotensin 1- 5;Angiotensin 1-4 A2M P01023 91 74 68,9 163,29 Alpha-2-macroglobulin C3 P01024;O95568 152 139 84,8 187,15 Complement C3;Complement C3 beta chain;C3-beta-c;Complement C3 alpha chain;C3a anaphylatoxin;Acylation stimulating protein;Complement C3b alpha chain;Complement C3c alpha chain fragment 1;Complement C3dg fragment;Complement C3g fragment;Complement C3d fragment;Complement C3f fragment;Complement C3c alpha chain fragment 2 C5 P01031;CON__Q1A7A4 68 68 49,5 188,3 Complement C5;Complement C5 beta chain;Complement C5 alpha chain;C5a anaphylatoxin;Complement C5 alpha chain TIMP1 P01033 8 8 57,5 23,171 Metalloproteinase inhibitor 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CST3 P01034 13 13 67,1 15,799 Cystatin-C CST1;CST4;CST2 P01037;P01036;P0922 4 4 34 16,387 Cystatin-SN;Cystatin-S;Cystatin-SA 8 CSTA P01040 2 2 33,7 11,006 Cystatin-A;Cystatin-A, N-terminally processed KNG1 P01042 29 4 44,9 71,957 -1;Kininogen-1 heavy chain;T-;;Lysyl- bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor KNG1 P01042-2;P01042-3 26 1 56,4 47,883 Kininogen-1;Kininogen-1 heavy chain;T-kinin;Bradykinin;Lysyl- bradykinin;Kininogen-1 light chain;Low molecular weight growth-promoting factor PDGFB P01127-2;P01127 1 1 5,3 25,502 -derived growth factor subunit B LDLR P01130-3;P01130- 5 5 10,1 76,855 Low-density lipoprotein receptor 6;P01130-4;P01130- 5;P01130;P01130-2 TGFB1 P01137 4 4 10,8 44,341 Transforming growth factor beta- 1;Latency-associated peptide GNRH1 P01148 2 2 30,4 10,38 Progonadoliberin-1;Gonadoliberin- 1;GnRH-associated peptide 1 OXT P01178 4 3 44,8 12,722 -neurophysin 1;Oxytocin;Neurophysin 1 AVP P01185 3 2 33,5 17,325 -neurophysin 2- copeptin;Arg-vasopressin;Neurophysin 2;Copeptin

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] POMC P01189 5 5 23,2 29,424 Pro- opiomelanocortin;NPP;Melanotropin gamma;Potential peptide;Corticotropin;Melanotropin alpha;Corticotropin-like intermediary peptide; beta;Lipotropin gamma;Melanotropin beta;Beta- endorphin;Met- PENK P01210 10 10 30,7 30,787 -A;Synenkephalin;Met- enkephalin;PENK(114-133);PENK(143- 183);Met-enkephalin-Arg-Gly-Leu;Leu- enkephalin;PENK(237-258);Met- enkephalin-Arg-Phe PDYN P01213 8 8 46,5 28,385 Proenkephalin-B;Alpha- ;Beta-neoendorphin;Big ;(1- 17);Dynorphin A(1-13);Dynorphin A(1- 8);Leu- enkephalin;Rimorphin; PRL P01236 5 5 31,3 25,876 Prolactin CALCA P06881;P01258- 1 1 14,8 13,898 gene-related peptide 2;P01258 1;Calcitonin;Calcitonin;Katacalcin VIP P01282-2;P01282 1 1 11,2 19,081 VIP peptides;Intestinal peptide PHV- 42;Intestinal peptide PHM- 27;Vasoactive intestinal peptide NPY P01303 3 3 22,7 10,851 Pro- Y;;C- flanking peptide of NPY IGF2 P01344;P01344- 5 5 33,9 20,14 -like growth factor II;Insulin-like 2;P01344-3 growth factor II;Insulin-like growth factor II Ala-25 Del;Preptin IGJ P01591 7 7 64,2 18,098 Immunoglobulin J chain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] P01594 2 1 31,5 11,939 Ig kappa chain V-I region AU P01597 2 2 10,2 11,418 Ig kappa chain V-I region DEE P01598;P01596 3 2 32,4 11,788 Ig kappa chain V-I region EU P01601 1 1 13,7 12,73 Ig kappa chain V-I region HK101 IGKV1-5 P01602 3 2 24,8 12,781 Ig kappa chain V-I region HK102 P01603 2 2 31,5 11,285 Ig kappa chain V-I region Ka P01605 3 2 31,5 11,834 Ig kappa chain V-I region Lay P01609 3 2 42,6 11,764 Ig kappa chain V-I region Scw P01610;P80362;P0160 3 2 36,1 11,84 Ig kappa chain V-I region WEA;Ig kappa 0 chain V-I region WAT;Ig kappa chain V- I region Hau P01611 3 3 37 11,608 Ig kappa chain V-I region Wes P01612 3 3 47,7 11,87 Ig kappa chain V-I region Mev P01613 2 2 30,4 11,745 Ig kappa chain V-I region Ni P01614 3 1 39,1 12,676 Ig kappa chain V-II region Cum P01615 1 1 11,5 12,059 Ig kappa chain V-II region FR P01616 1 1 21,4 10,825 Ig kappa chain V-II region MIL P01617;P06309 3 1 38,9 12,059 Ig kappa chain V-II region TEW;Ig kappa chain V-II region GM607 P01619 1 1 14,8 11,12 Ig kappa chain V-III region B6 P01620 6 2 66,1 11,775 Ig kappa chain V-III region SIE P01621 4 2 47 10,729 Ig kappa chain V-III region NG9 P01624 2 1 24,8 11,922 Ig kappa chain V-III region POM P01625 5 2 47,4 12,64 Ig kappa chain V-IV region Len P04208;P01700 1 1 11,9 11,725 Ig lambda chain V-I region WAH;Ig lambda chain V-I region HA P01701 2 2 18,9 11,453 Ig lambda chain V-I region NEW P01703 2 2 36,9 10,904 Ig lambda chain V-I region NEWM P01707 2 2 18,9 11,561 Ig lambda chain V-II region TRO

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] P01708 2 2 18,3 11,506 Ig lambda chain V-II region BUR P01714 2 2 25 11,392 Ig lambda chain V-III region SH P01715 1 1 23,6 11,305 Ig lambda chain V-IV region Bau P01716 1 1 23,6 11,334 Ig lambda chain V-IV region X P01717 1 1 17,8 11,517 Ig lambda chain V-IV region Hil P01719;P01720 3 3 38,9 11,342 Ig lambda chain V-V region DEL P01721;P06317 2 2 33,9 11,918 Ig lambda chain V-VI region AR;Ig lambda chain V-VI region SUT P01742 1 1 17,1 12,472 Ig heavy chain V-I region EU P01743 3 3 43,6 12,946 Ig heavy chain V-I region HG3 P01763 3 2 36 12,141 Ig heavy chain V-III region WEA P01764 4 3 41 12,582 Ig heavy chain V-III region VH26 P01766;P01777 4 2 51,7 13,227 Ig heavy chain V-III region BRO P01767 2 1 26,1 11,906 Ig heavy chain V-III region BUT P01771 1 1 9,1 13,437 Ig heavy chain V-III region HIL P01772 1 1 8,7 13,718 Ig heavy chain V-III region KOL P01773 1 1 9,2 12,265 Ig heavy chain V-III region BUR P01775 1 1 16 12,729 Ig heavy chain V-III region LAY P01778 1 1 16,4 12,339 Ig heavy chain V-III region ZAP P01780 2 2 16,5 12,32 Ig heavy chain V-III region JON P01781;P01782 4 4 40,5 11,771 Ig heavy chain V-III region GAL P01824 2 2 13,2 14,117 Ig heavy chain V-II region WAH PIGR P01833 14 14 21,1 83,283 Polymeric immunoglobulin receptor;Secretory component IGKC P01834 8 8 88,7 11,609 Ig kappa chain C region IGHG1 P01857 28 15 73,6 36,105 Ig gamma-1 chain C region IGHG2 P01859 24 12 69,9 35,9 Ig gamma-2 chain C region IGHG3 P01860 23 7 51,5 41,287 Ig gamma-3 chain C region IGHG4 P01861 16 9 69,1 35,94 Ig gamma-4 chain C region

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] IGHM P01871;P01871-2 17 7 47,8 49,306 Ig mu chain C region IGHA1 P01876 19 9 65,4 37,654 Ig alpha-1 chain C region IGHA2 P01877 14 4 63,5 36,526 Ig alpha-2 chain C region IGHD P01880;P01880-2 7 7 29,9 42,253 Ig delta chain C region HLA-DRA P01903;P01906 4 4 22,4 28,607 HLA class II histocompatibility antigen, DR alpha chain HBZ P02008 4 3 30,3 15,637 subunit zeta HBD P02042;CON__Q3SX09; 14 7 95,2 16,055 Hemoglobin subunit delta CON__P02070;P02100

MB P02144 6 6 50,6 17,184 COL1A1 P02452;CON__Q862S4 16 16 14,9 138,94 Collagen alpha-1(I) chain

COL3A1 P02461- 8 8 8,9 111,91 Collagen alpha-1(III) chain 2;P02461;CON__P0425 8 CRYAB P02511 2 2 10,9 20,159 Alpha-crystallin B chain SPTA1 P02549-2;P02549 19 19 11,5 279,67 alpha chain, erythrocytic 1 APOA1 P02647 39 38 82,8 30,777 Apolipoprotein A-I;Proapolipoprotein A-I;Truncated apolipoprotein A-I APOE P02649;CON__Q03247 34 34 77,3 36,154

APOA2 P02652 10 10 69 11,175 Apolipoprotein A-II;Proapolipoprotein A-II;Truncated apolipoprotein A-II APOC1 P02654 3 3 24,1 9,3318 Apolipoprotein C-I;Truncated apolipoprotein C-I APOC2 P02655 5 5 52,5 11,284 Apolipoprotein C-II APOC3 P02656 6 6 55,6 10,852 Apolipoprotein C-III

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FGA P02671- 27 27 56,2 69,756 alpha chain;Fibrinopeptide 2;P02671;CON__P0267 A; 2 FGB P02675;CON__P02676 33 33 63,5 55,928 Fibrinogen beta chain;Fibrinopeptide B;Fibrinogen beta chain FGG P02679-2;P02679 30 30 76,2 49,496 MBP P02686-6;P02686- 2 2 13,8 17,343 basic protein 5;P02686-4;P02686- 3;P02686 GYPA P02724-3;P02724- 1 1 26,5 13 -A 2;P02724 SLC4A1 P02730-2;P02730 3 3 5,3 94,194 Band 3 anion transport protein CRP P02741;P02741-2 5 5 23,7 25,038 C-reactive protein;C-reactive protein(1-205) APCS P02743 4 4 19,7 25,387 Serum amyloid P-component;Serum amyloid P-component(1-203) C1QA P02745 5 5 18 26,016 Complement C1q subcomponent subunit A C1QB P02746 9 9 46,2 26,721 Complement C1q subcomponent subunit B C1QC P02747 6 6 30,2 25,773 Complement C1q subcomponent subunit C C9 P02748;CON__Q3MHN 21 20 48,8 63,173 ;REV__Q4AC99 C9;Complement component C9a;Complement component C9b APOH P02749 19 17 57,4 38,298 Beta-2- 1 LRG1 P02750 12 12 42,9 38,177 Leucine-rich alpha-2-glycoprotein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FN1 P02751;P02751- 96 4 54,9 262,62 ;Anastellin;Ugl-Y1;Ugl- 3;P02751-8;P02751- Y2;Ugl-Y3 17;P02751-6;P02751- 5;P02751-14;P02751- 10;P02751-9;P02751- 4;P02751-12;P02751- 16;P02751-2

FN1 P02751-15;P02751- 93 1 53,3 272,32 Fibronectin;Anastellin;Ugl-Y1;Ugl- 7;P02751-13;P02751- Y2;Ugl-Y3 11 RBP4 P02753 11 11 76,1 23,01 Retinol-binding protein 4;Plasma retinol-binding protein(1-182);Plasma retinol-binding protein(1-181);Plasma retinol-binding protein(1-179);Plasma retinol-binding protein(1-176) AMBP P02760 17 17 52,8 38,999 Protein AMBP;Alpha-1- microglobulin;Inter-alpha- inhibitor light chain;Trypstatin ORM1 P02763 17 14 60,7 23,511 Alpha-1-acid glycoprotein 1 AHSG P02765;CON__P12763 13 13 52,6 39,324 Alpha-2-HS-glycoprotein;Alpha-2-HS- glycoprotein chain A;Alpha-2-HS- glycoprotein chain B TTR P02766 14 14 80,3 15,887

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GC P02774;P02774- 41 41 78,7 52,963 -binding protein 3;P02774- 2;CON__Q3MHN5;CON __ENSEMBL:ENSBTAP0 0000018229

PPBP P02775 4 4 26,6 13,894 Platelet basic protein;Connective tissue-activating peptide III;TC- 2;Connective tissue-activating peptide III(1-81);Beta- thromboglobulin;Neutrophil-activating peptide 2(74);Neutrophil-activating peptide 2(73);Neutrophil-activating peptide 2;TC-1;Neutrophil-activating peptide 2(1-66);Neutrophil-activating peptide 2(1-63) PF4;PF4V1 P02776;P10720 2 2 25,7 10,845 ;Platelet factor 4, short form;Platelet factor 4 variant;Platelet factor 4 variant(4-74);Platelet factor 4 variant(5-74);Platelet factor 4 variant(6-74) CXCL10 P02778 2 2 22,4 10,881 C-X-C motif chemokine 10;CXCL10(1- 73) TFRC P02786 15 15 24,1 84,87 receptor protein 1; protein 1, serum form TF P02787;CON__Q2HJF0; 95 95 85 77,063 Serotransferrin CON__Q29443;CON__ Q0IIK2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LTF P02788-2;P02788 4 4 9,5 73,16 Lactotransferrin;Lactoferricin- H;Kaliocin-1;Lactoferroxin- A;Lactoferroxin-B;Lactoferroxin-C HPX P02790 32 32 74,5 51,676 FTH1 P02794 3 3 24 21,225 Ferritin heavy chain;Ferritin heavy chain, N-terminally processed ANG P03950 5 5 32 16,55 F11 P03951;P03951-2 13 13 28 70,108 Coagulation factor XI;Coagulation factor XIa heavy chain;Coagulation factor XIa light chain KLKB1 P03952;P20718 25 25 46,6 71,369 ;Plasma kallikrein heavy chain;Plasma kallikrein light chain SLPI P03973 4 4 45,5 14,326 Antileukoproteinase C4BPA P04003 14 14 31,7 67,033 C4b-binding protein alpha chain VTN P04004 20 17 50,2 54,305 ;Vitronectin V65 subunit;Vitronectin V10 subunit;Somatomedin-B CAT P04040 17 17 41,7 59,755 Catalase GBA P04062-4;P04062- 5 5 12 50,316 Glucosylceramidase 2;P04062;P04062- 5;P04062-3 FUCA1 P04066 10 10 22,3 53,688 Tissue alpha-L-fucosidase PROC P04070;P04070-2 6 6 20,4 52,071 -dependent protein C;Vitamin K-dependent protein C light chain;Vitamin K-dependent protein C heavy chain;Activation peptide ALDOA P04075;P04075-2 18 15 74,5 39,42 Fructose-bisphosphate aldolase A CSTB P04080 3 3 45,9 11,139 Cystatin-B ANXA1 P04083 3 3 15,3 38,714 A1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PDGFA P04085-2;P04085 2 2 13,3 22,253 Platelet-derived growth factor subunit A APOB P04114 78 75 21,3 515,6 -100;Apolipoprotein B-48 PRNP P04156-2;P04156 9 9 39,8 26,885 Major prion protein SOD2 P04179- 5 5 25,6 19,73 Superoxide dismutase [Mn], 4;P04179;P04179- mitochondrial 2;P04179-3 LCAT P04180 9 9 32 49,577 Phosphatidylcholine-sterol acyltransferase HRG P04196 16 16 37 59,578 Histidine-rich glycoprotein P04206 4 1 55 11,83 Ig kappa chain V-III region GOL P04207 3 2 31 14,275 Ig kappa chain V-III region CLL P04209 1 1 8 11,581 Ig lambda chain V-II region NIG-84 P04211 1 1 7,7 12,38 Ig lambda chain V region 4A THY1 P04216 4 4 24,8 17,935 Thy-1 membrane glycoprotein A1BG P04217;P04217- 16 16 57,2 54,253 Alpha-1B-glycoprotein 2;CON__Q2KJF1 CD74 P04233 2 1 11,1 33,515 HLA class II histocompatibility antigen gamma chain S100B P04271 2 2 40,2 10,713 Protein S100-B VWF P04275;P04275-2 31 31 17,8 309,26 ;von Willebrand antigen 2 SHBG P04278;P04278- 11 10 36,8 43,779 Sex -binding globulin 4;P04278-2;P04278- 3;P04278-5 GAPDH P04406;P04406- 12 12 54 36,053 Glyceraldehyde-3-phosphate 2;O14556 dehydrogenase P04430 1 1 16,7 11,84 Ig kappa chain V-I region BAN P04433 3 3 27 12,575 Ig kappa chain V-III region VG

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] P04438;P01814 3 2 16,3 16,323 Ig heavy chain V-II region SESS HSPB1 P04792 4 4 36,1 22,782 Heat shock protein beta-1 RPN2 P04844-2;P04844 2 2 4,7 67,723 Dolichyl-diphosphooligosaccharide-- protein subunit 2 HIST1H2AJ;HIST1H2AH;H Q99878;Q96KK5;Q9BT 1 1 14,8 13,936 Histone H2A type 1-J;Histone H2A type 2AFJ;HIST2H2AC;HIST1H M1;Q16777;Q93077;Q 1-H;Histone H2A.J;Histone H2A type 2- 2AC;HIST3H2A;HIST2H2A 7L7L0;Q6FI13;P20671;P C;Histone H2A type 1-C;Histone H2A A3;HIST1H2AD;HIST1H2 0C0S8;P04908 type 3;Histone H2A type 2-A;Histone AG;HIST1H2AB H2A type 1-D;Histone H2A type 1;Histone H2A type 1-B/E

IGF1 P05019-3;P05019- 2 2 9,5 15,177 Insulin-like growth factor I 2;P05019-4;P05019 ATP1B1 P05026-2;P05026 4 4 17,9 34,893 Sodium/-transporting ATPase subunit beta-1 CHGB P05060 41 41 59,1 78,275 Secretogranin-1;GAWK peptide;CCB peptide ALDOB P05062 4 2 11,5 39,473 Fructose-bisphosphate aldolase B APP P05067-11;P05067- 28 26 41 84,52 Amyloid beta A4 protein;N- 8;P05067;P05067- APP;Soluble APP-alpha;Soluble APP- 7;P05067-9;P05067- beta;C99;Beta-amyloid protein 4;P05067-6;P05067- 42;Beta-amyloid protein 3;P05067-5;P05067- 40;C83;P3(42);P3(40);C80;Gamma- 10;P05067-2 secretase C-terminal fragment 59;Gamma-secretase C-terminal fragment 57;Gamma-secretase C- terminal fragment 50;C31

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] APOD P05090 12 12 52,9 21,275 ITGB2 P05107 4 4 9 84,781 Integrin beta-2 S100A8 P05109 4 4 39,8 10,834 Protein S100-A8;Protein S100-A8, N- terminally processed SERPINA5 P05154 15 15 39,4 45,674 Plasma serine protease inhibitor SERPING1 P05155;P05155- 22 22 41 55,154 Plasma protease C1 inhibitor 3;P05155- 2;CON__P50448 CFI P05156;CON__Q32PI4 26 26 45,1 65,75 ;Complement factor I heavy chain;Complement factor I light chain F13B P05160 19 19 40,2 75,51 Coagulation factor XIII B chain ICAM1 P05362 5 5 13,9 57,825 Intercellular adhesion molecule 1 RPLP2 P05387 2 2 24,3 11,665 60S acidic ribosomal protein P2 SCG5 P05408 9 1 51,4 23,729 Neuroendocrine protein 7B2;N- terminal peptide;C-terminal peptide SCG5 P05408-2 9 1 51,2 23,658 Neuroendocrine protein 7B2;N- terminal peptide;C-terminal peptide FABP3 P05413 4 4 28,6 14,858 Fatty acid-binding protein, CLEC3B P05452;CON__Q2KIS7 11 11 68,3 22,537 Tetranectin

HLA-A P05534 12 1 44,7 40,688 HLA class I histocompatibility antigen, A-24 alpha chain SERPINA7 P05543;CON__Q9TT36 16 16 48,4 46,324 Thyroxine-binding globulin

SERPIND1 P05546;CON__ENSEMB 21 21 58,7 57,07 cofactor 2 L:ENSBTAP0000001857 4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ITGB1 P05556- 6 6 9,9 87,445 Integrin beta-1 2;P05556;P05556- 5;P05556-4;P05556-3

CALB1 P05937;P05937-2 13 12 54,4 30,025 MYL1 P05976-2;P05976 2 2 12,7 16,684 light chain 1/3, isoform COL5A2 P05997 4 4 4,3 144,91 Collagen alpha-2(V) chain BCHE P06276 8 8 16,6 68,417 GLA P06280 6 6 21,2 48,766 Alpha-galactosidase A P06310 2 1 15 14,707 Ig kappa chain V-II region RPMI 6410 P06311 2 2 24,2 14,07 Ig kappa chain V-III region IARC/BL41 P06318;P06319 2 2 32,4 11,966 Ig lambda chain V-VI region WLT;Ig lambda chain V-VI region EB4 P06331;P01825 2 2 17,1 16,228 Ig heavy chain V-II region ARH-77;Ig heavy chain V-II region NEWM GSN P06396;P06396- 43 2 56,8 85,696 4;P06396-3 GSN P06396-2 43 2 59,6 80,64 Gelsolin C2 P06681;P06681- 28 28 47,3 83,267 Complement C2;Complement C2b 3;P06681-2 fragment;Complement C2a fragment S100A9 P06702 6 6 69,3 13,242 Protein S100-A9 APOA4 P06727;CON__Q32PJ2 37 37 80,6 45,398 Apolipoprotein A-IV

CKM P06732 11 11 36,2 43,101 Creatine kinase M-type;Creatine kinase M-type, N-terminally processed ENO1 P06733;P06733-2 19 16 57,1 47,168 Alpha-enolase GPI P06744;P06744-2 8 5 19 63,146 Glucose-6-phosphate isomerase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TPM3 P06753-5;P06753- 6 4 23,4 28,87 alpha-3 chain 2;P06753-4;P06753- 3;P06753- 6;P06753;P06753-7 CRH P06850 1 1 13,8 21,422 Corticoliberin LPL P06858 5 5 11,6 53,162 Lipoprotein HEXA P06865;P06865-2 16 16 33,3 60,702 Beta- subunit alpha P06888 1 1 13,8 11,414 Ig lambda chain V-I region EPS P06889 1 1 23,6 11,143 Ig lambda chain V-IV region MOL SERPINE2 P07093-2;P07093- 12 12 32,7 44 -derived nexin 3;P07093 DBI P07108;P07108- 3 3 50,6 10,044 Acyl-CoA-binding protein 3;P07108-2;P07108- 4;P07108-5;P07108-6

LDHB P07195 20 19 62,9 36,638 L-lactate dehydrogenase B chain NEFL P07196 4 3 8,5 61,516 light polypeptide NEFM P07197;P07197- 14 13 20,3 102,47 Neurofilament medium polypeptide 2;Q16352 PROS1 P07225;CON__P07224 26 26 47,8 75,122 Vitamin K-dependent

P4HB P07237 16 16 38,4 57,116 Protein disulfide-isomerase ACYP1 P07311 1 1 10,1 11,261 -1 CSF1R P07333;P07333-2 8 8 11,8 107,98 Macrophage colony-stimulating factor 1 receptor CTSD P07339 17 17 50,7 44,552 D;Cathepsin D light chain;Cathepsin D heavy chain ANXA2;ANXA2P2 P07355;P07355- 4 4 14,7 38,604 ;Putative annexin A2-like 2;A6NMY6 protein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] C8A P07357 16 16 42,3 65,163 Complement component C8 alpha chain C8B P07358 19 19 41,3 67,046 Complement component C8 beta chain GP1BA P07359 2 2 4,9 71,539 Platelet alpha chain;Glycocalicin C8G P07360 8 8 50,5 22,277 Complement component C8 gamma chain CAPN1 P07384 2 2 3,4 81,889 -1 catalytic subunit CA3 P07451 5 5 23,8 29,557 Carbonic anhydrase 3 PRSS2 P07478 2 1 12,1 26,487 Trypsin-2 GRP P07492- 3 3 22,7 15,532 -releasing 3;P07492;P07492-2 peptide;Neuromedin-C DCN P07585;P07585- 8 8 24,2 39,746 4;P07585-2;P07585- 5;P07585-3 PSAP P07602;P07602- 27 27 58,6 58,112 Prosaposin;Saposin-A;Saposin-B- 2;P07602-3 Val;Saposin-B;Saposin-C;Saposin-D HEXB P07686 16 16 36,7 63,111 Beta-hexosaminidase subunit beta;Beta-hexosaminidase subunit beta chain B;Beta-hexosaminidase subunit beta chain A CTSL P07711;Q5NE16;P4323 10 10 49,8 37,564 Cathepsin L1;Cathepsin L1 heavy 5;O60911 chain;Cathepsin L1 light chain PFN1 P07737;CON__P02584 7 7 60 15,054 -1

BPGM P07738 2 2 16,2 30,005 Bisphosphoglycerate mutase CTSB P07858 13 13 43,1 37,821 Cathepsin B;Cathepsin B light chain;Cathepsin B heavy chain HSP90AA1 P07900;P07900- 12 7 21 84,659 Heat shock protein HSP 90-alpha 2;Q14568

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LAMB1 P07942 32 32 29,5 198,04 Laminin subunit beta-1 SFTPB P07988 1 1 3,1 42,117 Pulmonary surfactant-associated protein B RNASE1 P07998 7 7 62,8 17,644 Ribonuclease pancreatic COL1A2 P08123 16 16 15,5 129,31 Collagen alpha-2(I) chain ANXA6 P08133-2;P08133 4 4 8,4 72,423 RHOA;RHOC;RHOB P61586;P08134;P6274 1 1 8,8 21,768 Transforming protein RhoA;Rho- 5 related GTP-binding protein RhoC;Rho- related GTP-binding protein RhoB NGFR P08138-2;P08138 2 2 8,1 35,766 Tumor necrosis factor receptor superfamily member 16 CD55 P08174- 14 14 37,6 39,759 Complement decay-accelerating factor 4;P08174;P08174- 3;P08174-5;P08174- 2;P08174-6;P08174-7

SERPINA6 P08185 13 13 43,5 45,14 Corticosteroid-binding globulin SLC3A2 P08195-2;P08195- 16 16 39,3 57,944 4F2 cell-surface antigen heavy chain 3;P08195;P08195-4 HSP90AB1 P08238;Q58FF7;Q58FG 10 3 15,1 83,263 Heat shock protein HSP 90-beta 0;Q58FF8;Q58FG1;Q58 FF6 MMP2 P08253;P08253- 28 28 60,2 73,881 72 kDa type IV ;PEX 3;P08253-2;P09237 MMP3 P08254;P09238 4 4 7,5 53,977 Stromelysin-1 SOD3 P08294 7 7 37,1 25,851 Extracellular superoxide dismutase [Cu-Zn] HMBS P08397-4;P08397- 1 1 5,6 33,264 Porphobilinogen deaminase 3;P08397-2;P08397 MME P08473 1 1 1,3 85,513

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] INHBA P08476 1 1 4,2 47,442 Inhibin beta A chain MGP P08493;P08493-2 2 2 21,4 12,353 LPA P08519 3 2 18,8 501,31 Apolipoprotein(a) CD14 P08571 13 13 45,6 40,076 Monocyte differentiation antigen CD14;Monocyte differentiation antigen CD14, urinary form;Monocyte differentiation antigen CD14, membrane-bound form COL4A2 P08572 13 13 12 167,55 Collagen alpha-2(IV) chain;Canstatin PTPRC P08575-2;P08575 5 5 5,2 130,9 Receptor-type tyrosine-protein phosphatase C MET P08581- 5 5 10,2 85,744 receptor 3;P08581;P08581-2 MFI2 P08582;P08582-2 10 10 20,1 80,214 Melanotransferrin CFH P08603;P08603-2 62 56 58,8 139,09 Complement FCGR3A P08637 4 3 17,7 29,089 Low affinity immunoglobulin gamma Fc region receptor III-A VIM P08670 18 15 41,2 53,651 SERPINF2 P08697;P08697- 17 17 38,9 54,565 Alpha-2-antiplasmin 2;CON__P28800 ANXA5 P08758 7 7 24,7 35,936 IL6R P08887-2;P08887 2 2 8,2 40,237 -6 receptor subunit alpha NMB P08949;P08949-2 1 1 11,6 13,251 Neuromedin-B;Neuromedin-B- 32;Neuromedin-B ENO2 P09104;P09104-2 16 12 60,8 47,268 Gamma-enolase DBH P09172 10 10 23,7 69,064 Dopamine beta-hydroxylase;Soluble dopamine beta-hydroxylase GSTP1 P09211 10 10 60,5 23,356 Glutathione S- P LGALS1 P09382 5 5 43,7 14,716 Galectin-1 QDPR P09417;P09417-2 9 9 57 25,789 Dihydropteridine reductase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FBP1 P09467 2 2 8,9 36,842 Fructose-1,6-bisphosphatase 1 SPARC P09486 15 15 48,5 34,632 SPARC GSTM1;GSTM4;GSTM2;G P09488- 2 2 13,3 21,252 Glutathione S-transferase Mu STM5 2;P09488;Q03013- 1;Glutathione S-transferase Mu 3;P28161-2;Q03013- 4;Glutathione S-transferase Mu 2;Q03013;P28161;P464 2;Glutathione S-transferase Mu 5 39

TPM1 P09493-4;P09493- 5 1 17,3 32,847 Tropomyosin alpha-1 chain 10;P09493;P09493- 9;P09493-3 TPM1 P09493-6;P09493- 5 1 18,3 32,649 Tropomyosin alpha-1 chain 8;P09493-7;P09493- 2;P09493-5 INHBB P09529 1 1 2,5 45,121 Inhibin beta B chain CSF1 P09603;P09603- 10 10 24,9 60,179 Macrophage colony-stimulating factor 2;P09603-3 1;Processed macrophage colony- stimulating factor 1 PDGFRB P09619;P09619-2 11 11 11,6 123,97 Platelet-derived growth factor receptor beta DLD P09622- 6 6 19,5 43,587 Dihydrolipoyl dehydrogenase, 2;P09622;P09622-3 mitochondrial CTSH P09668 10 10 38,5 37,393 Pro-cathepsin H;Cathepsin H mini chain;Cathepsin H;Cathepsin H heavy chain;Cathepsin H light chain C1S P09871 31 31 52,8 76,684 Complement C1s subcomponent;Complement C1s subcomponent heavy chain;Complement C1s subcomponent light chain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] UCHL1 P09936 3 3 25,6 24,824 Ubiquitin carboxyl-terminal hydrolase isozyme L1 P09958 2 2 4,2 86,677 Furin LTA4H P09960;P09960- 12 12 26,8 69,284 Leukotriene A-4 hydrolase 4;P09960-2;P09960-3

ALDOC P09972 19 15 73,1 39,455 Fructose-bisphosphate aldolase C C4A P0C0L4;P0C0L4-2 97 5 62,7 192,78 Complement C4-A;Complement C4 beta chain;Complement C4-A alpha chain;C4a anaphylatoxin;C4b-A;C4d- A;Complement C4 gamma chain C4B P0C0L5 97 6 62,5 192,75 Complement C4-B;Complement C4 beta chain;Complement C4-B alpha chain;C4a anaphylatoxin;C4b-B;C4d- B;Complement C4 gamma chain LINGO3 P0C6S8 6 6 11,7 64,88 Leucine-rich repeat and immunoglobulin-like domain- containing nogo receptor-interacting protein 3 ELFN1 P0C7U0 2 2 4,6 90,476 Protein ELFN1 ASAH2B;ASAH2 P0C7U1- 1 1 9,4 18,025 Putative inactive neutral 2;P0C7U1;Q9NR71- B;Neutral ceramidase;Neutral 2;Q9NR71 ceramidase soluble form IGLC2;IGLC3 P0CG05;P0CG06;P0CF7 9 3 93,4 11,293 Ig lambda-2 chain C regions;Ig lambda- 4 3 chain C regions

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] UBA52;RPS27A;UBB;UBC P62987;P62979;P0CG4 8 8 51,6 14,728 Ubiquitin-60S ribosomal protein 7;P0CG48 L40;Ubiquitin;60S ribosomal protein L40;Ubiquitin-40S ribosomal protein S27a;Ubiquitin;40S ribosomal protein S27a;Polyubiquitin- B;Ubiquitin;Polyubiquitin-C;Ubiquitin SAA1 P0DJI8;P0DJI9-2;P0DJI9 3 3 40,2 13,532 Serum amyloid A-1 protein;Amyloid protein A;Serum amyloid protein A(2- 104);Serum amyloid protein A(3- 104);Serum amyloid protein A(2- 103);Serum amyloid protein A(2- 102);Serum amyloid protein A(4-101) P0DMQ5 5 5 19 15,439 P0DMV9;P0DMV8;P0D 16 8 34,6 70,051 MV8-2 CALCB P10092 2 2 22 13,706 Calcitonin gene-related peptide 2 RAP2A;RAP2C;RAP2B P10114;Q9Y3L5;P6122 2 2 12 20,615 Ras-related protein Rap-2a;Ras-related 5 protein Rap-2c;Ras-related protein Rap-2b SRGN P10124 4 4 31,6 17,652 Serglycin CXCL8 P10145 1 1 16,2 11,098 Interleukin-8;MDNCF-a;Interleukin- 8;IL-8(5-77);IL-8(6-77);IL-8(7-77);IL- 8(8-77);IL-8(9-77) RNASE2 P10153 4 4 21,1 18,354 Non-secretory ribonuclease GAA P10253 9 9 12,4 105,32 Lysosomal alpha-glucosidase;76 kDa lysosomal alpha-glucosidase;70 kDa lysosomal alpha-glucosidase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HIST1H1C;HIST1H1E;HIST P16403;P10412;P1640 2 2 10,8 21,364 Histone H1.2;Histone H1.4;Histone 1H1D;HIST1H1T;HIST1H1 2;P22492;Q02539 H1.3;Histone H1t;Histone H1.1 A

SPP1 P10451- 15 2 53,8 33,016 4;P10451;CON__P3109 6 SPP1 P10451-3 13 2 45,3 32,355 Osteopontin SPP1 P10451-5 14 1 47,7 33,843 Osteopontin PTPRF P10586-2;P10586 30 28 24,4 211,68 Receptor-type tyrosine-protein phosphatase F TXN P10599;P10599-2 6 6 55,2 11,737 Thioredoxin CTSA P10619-2;P10619 4 4 11 52,488 Lysosomal protective protein;Lysosomal protective protein 32 kDa chain;Lysosomal protective protein 20 kDa chain MAPT P10636-5;P10636- 4 1 15,6 42,603 -associated protein tau 8;P10636;P10636-9 MAPT P10636-4;P10636- 4 1 19,4 39,72 Microtubule-associated protein tau 7;P10636-3;P10636- 2;P10636-6 C7 P10643;CON__Q29RQ1 36 35 55,3 93,517 Complement component C7

PRKAR1A P10644;P10644-2 8 7 25,2 42,981 cAMP-dependent protein kinase type I-alpha regulatory subunit;cAMP- dependent protein kinase type I-alpha regulatory subunit, N-terminally processed

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CHGA P10645 25 25 68,5 50,688 Chromogranin-A;Vasostatin- 1;Vasostatin-2;EA-92;ES- 43;Pancreastatin;SS-18;WA-8;WE- 14;LF-19;AL-11;GV-19;GR-44;ER-37 TFPI P10646;P10646-2 3 3 12,8 35,015 pathway inhibitor KIT P10721- 10 10 11,7 109,45 Mast/ growth factor receptor 2;P10721;P10721-3 Kit RBP3 P10745 16 16 21,3 135,36 Retinol-binding protein 3 ESD P10768 5 5 20,6 31,462 S-formylglutathione hydrolase HSPD1 P10809 2 2 3,7 61,054 60 kDa heat shock protein, mitochondrial CLU P10909- 28 28 48,8 48,803 ;Clusterin beta chain;Clusterin 4;P10909;P10909- alpha chain 5;P10909-2;P10909-3

HSPA5 P11021 26 25 43,7 72,332 78 kDa glucose-regulated protein LAMC1 P11047 38 38 35,6 177,6 Laminin subunit gamma-1 ACP2 P11117;P11117-2 3 3 8,5 48,344 Lysosomal MAP2 P11137-3;P11137 3 3 2,2 199,08 Microtubule-associated protein 2 HSPA8 P11142;P11142-2 14 11 29,1 70,897 Heat shock cognate 71 kDa protein EPB41 P11171-4;P11171- 3 3 10 66,398 Protein 4.1 3;P11171-7;P11171- 2;P11171;P11171- 6;P11171-5 ITGAM P11215;P11215-2 4 4 4,4 127,18 Integrin alpha-M PYGB P11216 1 1 1,2 96,695 , brain form SPTB P11277- 10 10 6,7 242,8 Spectrin beta chain, erythrocytic 3;P11277;P11277-2 LAMP1 P11279;P11279-2 5 5 12,2 44,882 Lysosome-associated membrane glycoprotein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FGFR1 P11362-9;P11362- 10 10 15,2 73,274 receptor 1 8;P11362-20;P11362- 2;P11362;P11362- 16;P11362-11;P11362- 10;P11362-4;P11362- 3;P11362-7;P11362- 19;P11362-21;P11362- 18;P11362-13;P11362- 12;P11362-6;P11362- 5;P11362-14;P11362- 15

CETP P11597-2;P11597 2 2 5,3 47,787 Cholesteryl transfer protein SCGB1A1 P11684 2 2 12,1 9,9937 IGF2R P11717 25 25 14,7 274,37 Cation-independent mannose-6- phosphate receptor ADH5 P11766 3 3 11,2 39,724 Alcohol dehydrogenase class-3 NEFH P12036-2;P12036 3 2 3,6 105,64 Neurofilament heavy polypeptide COL11A1 P12107-4;P12107- 6 6 5,3 167,75 Collagen alpha-1(XI) chain 3;P12107;P12107-2 COL6A1 P12109 38 38 53,5 108,53 Collagen alpha-1(VI) chain COL6A2 P12110 12 1 17,2 108,58 Collagen alpha-2(VI) chain COL6A2 P12110-2;P12110-3 12 1 19,1 97,418 Collagen alpha-2(VI) chain COL6A3 P12111;P12111- 74 7 31 343,67 Collagen alpha-3(VI) chain 2;P12111-5;P12111-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] F5 P12259 56 48 28,8 251,7 Coagulation ;Coagulation factor V heavy chain;Coagulation factor V light chain CKB P12277 6 6 22 42,644 Creatine kinase B-type FCGR2A;FCGR2C P12318- 2 2 9,8 34,929 Low affinity immunoglobulin gamma 2;P12318;P31995 Fc region receptor II-a;Low affinity immunoglobulin gamma Fc region receptor II-c CKMT1A P12532;P12532-2 5 5 16,8 47,036 Creatine kinase U-type, mitochondrial BMP4 P12644 1 1 6,1 46,554 morphogenetic protein 4 ACTN1;ACTN2 P12814- 4 2 5,5 102,71 Alpha--1;Alpha-actinin-2 2;P12814;P12814- 3;P12814-4;P35609- 2;P35609 ACE P12821- 13 13 16,7 131,66 Angiotensin-converting 2;P12821;P12821- ;Angiotensin-converting 4;P12821-3 enzyme, soluble form CDH1 P12830;P12830-2 7 7 12,9 97,455 -1;E-Cad/CTF1;E-Cad/CTF2;E- Cad/CTF3 MYH7;MYH6 P12883;P13533 3 3 2,6 223,09 Myosin-7;Myosin-6 PEPD P12955;P12955- 7 7 18,5 54,548 Xaa-Pro 3;P12955-2 IFI30 P13284 1 1 10,4 27,963 Gamma-interferon-inducible lysosomal reductase TDGF1P3;TDGF1 P51864;P13385 1 1 8 21,18 Putative teratocarcinoma-derived growth factor 3;Teratocarcinoma- derived growth factor 1 LAMP2 P13473- 5 5 13,7 44,955 Lysosome-associated membrane 2;P13473;P13473-3 glycoprotein 2 RNH1 P13489 5 5 17,1 49,973 Ribonuclease inhibitor

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] BMP1 P13497-3;P13497- 2 2 8,9 33,424 Bone morphogenetic protein 1 4;P13497-5;P13497- 2;P13497-6;P13497 CCL2 P13500 1 1 11,1 11,025 C-C motif chemokine 2 SCG2 P13521 34 34 66,9 70,94 Secretogranin-2;Secretoneurin NCAM1 P13591;P13591- 34 1 46,5 94,573 Neural cell adhesion molecule 1 5;P13591-6 ICAM2 P13598 4 4 18,2 30,654 Intercellular adhesion molecule 2 VCAN P13611;P13611- 23 23 8,4 372,82 core protein 5;P13611-3;P13611- 2;P13611-4 ATP1A3 P13637;P13637- 4 1 6,5 111,75 Sodium/potassium-transporting 2;P13637- ATPase subunit alpha-3 3;Q13733;P54707;P547 07-2 EEF2 P13639 4 4 6,9 95,337 2 PDIA4 P13667 16 15 29,5 72,932 Protein disulfide-isomerase A4 C6 P13671 28 28 38,3 104,79 Complement component C6 TPT1 P13693;P13693- 4 4 30,2 19,595 Translationally-controlled tumor 2;Q56UQ5 protein ALAD P13716;P13716-2 2 2 8,8 36,294 Delta-aminolevulinic acid dehydratase F3 P13726-2;P13726 1 1 8,4 27,145 Tissue factor HLA-E P13747 3 1 11,5 40,156 HLA class I histocompatibility antigen, alpha chain E HLA-DRB1 P13760;Q30167;Q3015 3 2 14,3 30,112 HLA class II histocompatibility antigen, 4;Q29974;P04229 DRB1-4 beta chain

LCP1 P13796;P13796-2 18 14 35,7 70,288 Plastin-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PLS3 P13797;P13797- 12 8 23,8 70,81 Plastin-3 3;P13797-2;Q14651

APEH P13798 4 4 7,8 81,224 Acylamino-acid-releasing enzyme PRKAR2A P13861-2;P13861 1 1 5,2 43,066 cAMP-dependent protein kinase type II-alpha regulatory subunit ENO3 P13929-3;P13929- 7 3 26,9 42,248 Beta-enolase 2;P13929 CD59 P13987 5 5 37,5 14,177 CD59 glycoprotein GFAP P14136- 8 8 15,5 49,507 Glial fibrillary acidic protein 3;P14136;P14136-2 EDN3 P14138;P14138-3 3 1 17,6 25,454 Endothelin-3 SELL P14151;P14151-2 7 7 16,9 42,187 L- MIF P14174 3 3 35,7 12,476 Macrophage migration inhibitory factor FOLR2 P14207;P41439- 9 9 40,4 29,279 Folate receptor beta 2;P41439 CD99 P14209- 2 2 37,5 16,015 CD99 antigen 2;P14209;P14209-3 PRKCSH P14314-2;P14314 17 17 33,7 59,177 Glucosidase 2 subunit beta FDPS P14324-2;P14324 2 2 7,9 40,532 Farnesyl pyrophosphate synthase CPM P14384 6 6 18,3 50,513 NID1 P14543;P14543-2 30 29 37 136,38 Nidogen-1 AKR1A1 P14550 4 4 19,7 36,573 Alcohol dehydrogenase [NADP(+)] PKM P14618;P14618-3 31 1 60,3 57,936 Pyruvate kinase PKM PKM P14618-2 34 4 66,5 58,061 Pyruvate kinase PKM ACYP2 P14621 6 6 45,5 11,139 Acylphosphatase-2 HSP90B1 P14625 26 24 40,3 92,468 Endoplasmin CPB1 P15086 6 6 17,3 47,367

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FABP4 P15090 5 5 37,1 14,719 Fatty acid-binding protein, adipocyte AKR1B1 P15121 6 6 23,1 35,853 ANPEP P15144 11 11 14,5 109,54 N PVR P15151-3;P15151- 5 5 17,3 39,304 Poliovirus receptor 2;P15151-4;P15151 CPN1 P15169;CON__Q2KJ83 6 6 19,2 52,286 Carboxypeptidase N catalytic chain

PGAM2 P15259 4 1 20,2 28,766 Phosphoglycerate mutase 2 ARSA P15289-2;P15289 7 7 26,2 44,881 A; component B;Arylsulfatase A component C B4GALT1 P15291-2;P15291 9 9 43,9 42,537 Beta-1,4- 1; A protein;N- acetyllactosamine synthase;Beta-N- acetylglucosaminylglycopeptide beta- 1,4-galactosyltransferase;Beta-N- acetylglucosaminyl- beta-1,4- galactosyltransferase;Processed beta- 1,4-galactosyltransferase 1 ACPP P15309;P15309-2 1 1 2,6 44,566 Prostatic acid phosphatase;PAPf39 EZR P15311 13 4 22 69,412 Ezrin FOLR1 P15328 4 4 19,1 29,819 Folate receptor alpha ELN P15502-5;P15502- 6 3 13,9 61,604 2;P15502-1;P15502- 4;P15502-7;P15502- 6;P15502-12;P15502- 13;P15502- 10;P15502;P15502-9

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ELN P15502-8;P15502-11 4 1 11,1 56,55 Elastin

CSF2RA P15509-8;P15509- 4 4 21,3 31,101 Granulocyte-macrophage colony- 3;P15509- stimulating factor receptor subunit 5;P15509;P15509- alpha 2;P15509-7;P15509- 4;P15509-6 CD46 P15529-16;P15529- 2 2 6,8 36,826 Membrane cofactor protein 15;P15529-9;P15529- 7;P15529-12;P15529- 14;P15529-8;P15529- 4;P15529-6;P15529- 11;P15529-13;P15529- 3;P15529-5;P15529- 10;P15529;P15529-2

GNS P15586-2;P15586 7 7 14,3 59,988 N-acetylglucosamine-6- IGLL1 P15814 2 2 16 22,963 Immunoglobulin lambda-like polypeptide 1 ARSB P15848;P15848-2 2 2 5,6 59,687 TIMP2 P16035 14 14 55,5 24,399 Metalloproteinase inhibitor 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CD44 P16070-15;P16070- 4 4 18,7 32,074 CD44 antigen 18;P16070-12;P16070- 14;P16070-13;P16070- 11;P16070-10;P16070- 16;P16070-8;P16070- 9;P16070-17;P16070- 6;P16070-4;P16070- 3;P16070-7;P16070- 5;P16070;P16070-19

NQO2 P16083 5 5 29,4 25,918 Ribosyldihydronicotinamide dehydrogenase [quinone] ACAN P16112-3;P16112- 8 8 5,7 239,23 core protein;Aggrecan core 2;P16112 protein 2 ITGB4 P16144-5;P16144- 2 2 3 106,78 Integrin beta-4 4;P16144-2;P16144- 3;P16144 CBR1 P16152;P16152-2 12 10 64,3 30,375 Carbonyl reductase [NADPH] 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ANK1 P16157-2;P16157- 3 3 3 166,48 -1 11;P16157-9;P16157- 6;P16157-7;P16157- 4;P16157-13;P16157- 10;P16157-15;P16157- 8;P16157-5;P16157- 16;P16157- 3;P16157;P16157- 21;P16157-12;P16157- 14

PDGFRA P16234- 3 3 6,7 82,808 Platelet-derived growth factor 3;P16234;P16234-2 receptor alpha GLB1 P16278- 4 4 7 72,75 Beta-galactosidase 3;P16278;P16278-2 PECAM1 P16284-5;P16284- 2 2 2,8 79,26 Platelet endothelial cell adhesion 3;P16284-4;P16284- molecule 2;P16284-6;P16284 EPB42 P16452- 1 1 3,1 69,455 Erythrocyte membrane protein band 3;P16452;P16452-2 4.2 PCSK2 P16519-2;P16519- 14 14 30 66,312 Neuroendocrine convertase 2 3;P16519 CPE P16870-2;P16870 23 23 64,3 49,885 FAH P16930;P16930-2 2 2 4,5 46,374 Fumarylacetoacetase STMN1 P16949;P16949- 6 6 30,9 17,302 2;Q93045;Q93045-2

NAGA P17050 3 3 9 46,564 Alpha-N-acetylgalactosaminidase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GOT1 P17174;P17174-2 22 22 66,6 46,247 Aspartate aminotransferase, cytoplasmic IFNAR1 P17181-2;P17181- 2 2 6,5 49,546 Interferon alpha/beta receptor 1 3;P17181;P17181-4 SMPD1 P17405-3;P17405- 2 2 3,7 63,51 2;P17405-4;P17405 SYN1 P17600- 3 3 7,9 70,032 Synapsin-1 2;P17600;Q92777- 2;Q92777 PRKACA P17612-2;P17612 1 1 5,5 39,821 cAMP-dependent protein kinase catalytic subunit alpha GAP43 P17677;P17677-2 4 4 36,1 24,802 Neuromodulin HLA-G P17693 2 1 6,8 38,224 HLA class I histocompatibility antigen, alpha chain G ENG P17813-2;P17813 5 5 10,2 67,541 GM2A P17900 13 13 63,2 20,838 GM2 activator;Ganglioside GM2 activator isoform short LGALS3 P17931 2 2 9,6 26,152 Galectin-3 IGFBP3 P17936;P17936-2 11 11 50,2 31,674 Insulin-like growth factor-binding protein 3 IGFBP2 P18065 15 15 64,3 34,814 Insulin-like growth factor-binding protein 2 BMP7 P18075 2 2 5,3 49,312 Bone morphogenetic protein 7 P18135;P18136 7 1 65,9 14,073 Ig kappa chain V-III region HAH;Ig kappa chain V-III region HIC VCL P18206- 12 12 17 116,72 2;P18206;P18206-3 LBP P18428 9 9 28,3 53,383 Lipopolysaccharide-binding protein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ADCYAP1 P18509 2 2 27,8 18,835 Pituitary adenylate cyclase-activating polypeptide;PACAP-related peptide;Pituitary adenylate cyclase- activating polypeptide 27;Pituitary adenylate cyclase-activating polypeptide 38 PGAM1 P18669;Q8N0Y7 12 9 62,2 28,804 Phosphoglycerate mutase 1 SDC1 P18827 1 1 5,5 32,461 Syndecan-1 ATF4 P18848 2 2 9,7 38,589 Cyclic AMP-dependent factor ATF-4 ATF6 P18850 2 2 3,6 74,584 Cyclic AMP-dependent transcription factor ATF-6 alpha;Processed cyclic AMP-dependent transcription factor ATF-6 alpha PAM P19021- 43 2 57 106,27 Peptidyl-glycine alpha-amidating 6;P19021;P19021- monooxygenase;Peptidylglycine alpha- 5;P19021-4;P19021-2 hydroxylating monooxygenase;Peptidyl-alpha- hydroxyglycine alpha-amidating PAM P19021-3 42 1 59,7 100,82 Peptidyl-glycine alpha-amidating monooxygenase;Peptidylglycine alpha- hydroxylating monooxygenase;Peptidyl-alpha- hydroxyglycine alpha-amidating lyase CDH2 P19022;P19022-2 20 20 24,8 99,808 Cadherin-2 CD58 P19256-2;P19256- 1 1 4,2 26,66 Lymphocyte function-associated 3;P19256 antigen 3 VCAM1 P19320;P19320- 29 29 49 81,275 Vascular cell adhesion protein 1 3;P19320-2;P49454

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HK1 P19367-4;P19367- 19 19 24,5 101,08 Hexokinase-1 2;P19367;P19367- 3;Q2TB90;P52789 TNFRSF1A P19438-5;P19438- 2 2 17,9 24,194 Tumor necrosis factor receptor 4;P19438 superfamily member 1A;Tumor necrosis factor receptor superfamily member 1A, membrane form;Tumor necrosis factor-binding protein 1 FUT1 P19526 1 1 3,6 41,251 Galactoside 2-alpha-L- 1 SLC9A1 P19634 2 2 5,5 90,762 Sodium/hydrogen exchanger 1 ORM2 P19652 12 9 55,7 23,602 Alpha-1-acid glycoprotein 2 ITIH2 P19823;CON__Q9TRI1 28 28 42,6 106,46 Inter-alpha- heavy chain H2 ITIH1 P19827;P19827- 27 27 39 101,39 Inter-alpha-trypsin inhibitor heavy 2;P19827- chain H1 3;CON__Q0VCM5 CEL P19835;P19835-2 9 9 15,8 79,321 Bile salt-activated lipase FST P19883-2;P19883 1 1 4,1 34,803 Follistatin AMY2B;AMY2A;AMY1A P19961;P19961- 7 7 18,4 57,709 Alpha-amylase 2B;Pancreatic alpha- 2;P04746;P04745;P047 amylase;Alpha-amylase 1 46-2;CON__Q3MHH8

HLA-DPA1 P20036 2 2 11,2 29,38 HLA class II histocompatibility antigen, DP alpha 1 chain HLA-DRB1 P20039;Q30134 2 1 7,1 30,16 HLA class II histocompatibility antigen, DRB1-11 beta chain;HLA class II histocompatibility antigen, DRB1-8 beta chain TCN2 P20062;P20062-2 15 15 34,4 47,534 -2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CD33 P20138-3;P20138- 1 1 5,5 25,293 Myeloid cell surface antigen CD33 2;P20138 TNFRSF1B P20333-2;P20333 1 1 11,2 28,461 Tumor necrosis factor receptor superfamily member 1B;Tumor necrosis factor receptor superfamily member 1b, membrane form;Tumor necrosis factor-binding protein 2 RAB6A;RAB6B;RAB39A P20340-4;Q9NRW1- 1 1 6,3 19,934 Ras-related protein -6A;Ras-related 2;Q9NRW1;P20340- protein Rab-6B;Ras-related protein 2;P20340;Q14964 Rab-39A TAC1 P20366- 2 2 21,6 13,036 Protachykinin-1;Substance 2;P20366;P20366- P;;Neuropeptide 4;P20366-3 K;Neuropeptide gamma;C-terminal- flanking peptide PMCH P20382 2 2 14,5 18,679 Pro-MCH;Neuropeptide-glycine- glutamic acid;Neuropeptide-glutamic acid-isoleucine;Melanin-concentrating hormone TRH P20396 7 7 37,2 27,404 Pro-thyrotropin-releasing hormone;Thyrotropin-releasing hormone PVALB P20472 7 7 65,5 12,059 alpha PSMB1 P20618 3 3 21,2 26,489 Proteasome subunit beta type-1 PZP P20742;P20742-2 31 21 28 163,86 Pregnancy zone protein OGN P20774 18 18 53 33,922 Mimecan CAST P20810-3;P20810- 6 6 16,1 63,665 4;P20810-8;P20810- 2;P20810;P20810- 9;P20810-5;P20810- 10;P20810-7;P20810-6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] EFNA1 P20827;P20827-2 4 4 19,5 23,787 Ephrin-A1;Ephrin-A1, secreted form C4BPB P20851-2;P20851 4 4 26,7 28,286 C4b-binding protein beta chain COL5A1 P20908 12 12 10,1 183,56 Collagen alpha-1(V) chain MAG P20916- 7 7 15,3 66,223 Myelin-associated glycoprotein 3;P20916;P20916-2 AGA P20933 3 3 13 37,208 N(4)-(beta-N-acetylglucosaminyl)-L- asparaginase;Glycosylasparaginase alpha chain;Glycosylasparaginase beta chain PTMS P20962 1 1 10,8 11,53 Parathymosin PTN P21246 6 6 39,9 18,942 GSTM3 P21266 2 2 12 26,559 Glutathione S-transferase Mu 3 CSRP1 P21291 3 3 25,4 20,567 Cysteine and glycine-rich protein 1 FLNA P21333- 37 35 22,8 280,01 -A 2;P21333;O75369- 5;O75369-4;O75369- 6;O75369-3;O75369- 2;O75369- 9;O75369;O75369-8

S1PR1 P21453 1 1 3,7 42,81 1-phosphate receptor 1 CNR1 P21554;P21554-3 2 2 6,8 52,857 receptor 1 SYT1 P21579 7 5 18,7 47,573 -1 KITLG P21583- 2 2 6,5 27,867 Kit ligand;Soluble KIT ligand 2;P21583;P21583-3 NT5E P21589-2;P21589 3 3 8,8 57,948 5-nucleotidase MDK P21741;P21741-2 2 2 24,5 15,585

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FGFR2 P21802-19;P21802- 6 6 19,7 40,613 Fibroblast growth factor receptor 2 15;P21802-8;P21802- 2;P21802-13;P21802- 17;P21802-12;P21802- 6;P21802-7;P21802- 9;P21802-5;P21802- 10;P21802- 18;P21802;P21802- 3;P21802-16;P21802- 11;P21802-14;P21802- 23;P21802-22;P21802- 4;P21802-20;P21802- 21

BGN P21810 10 10 37,5 41,654 ERBB3 P21860- 4 4 5,2 141,75 Receptor tyrosine-protein kinase erbB- 4;P21860;P21860-3 3 CD9 P21926 2 2 4,4 25,416 CD9 antigen BMP6 P22004 2 2 5,3 57,225 Bone morphogenetic protein 6 PCMT1 P22061;P22061-2 8 8 54,6 24,636 Protein-L-isoaspartate(D-aspartate) O- methyltransferase TNXB P22105;P22105- 65 65 23,5 458,22 Tenascin-X 3;P22105-4;P22105- 2;Q16473 CDH3 P22223-2;P22223 2 2 5,6 86,551 Cadherin-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ACHE P22303;P22303- 5 5 13,8 67,795 4;P22303-2;P22303-3

IDS P22304;P22304- 16 16 36 61,872 Iduronate 2-sulfatase;Iduronate 2- 2;P22304-3 sulfatase 42 kDa chain;Iduronate 2- sulfatase 14 kDa chain UBA1 P22314-2;P22314 4 4 4,2 113,8 Ubiquitin-like modifier-activating enzyme 1 GPX3 P22352 6 6 31 25,552 Glutathione peroxidase 3 NME2;NME1;NME2P1 P22392- 4 4 26,2 30,137 Nucleoside diphosphate kinase 2;P22392;P15531;P155 B;Nucleoside diphosphate kinase 31-2;O60361 A;Putative nucleoside diphosphate kinase FGFR3 P22607-3;P22607- 8 8 21,3 75,695 Fibroblast growth factor receptor 3 4;P22607;P22607- 2;P22455-3;P22455- 2;P22455 CALB2 P22676 4 3 17 31,54 IGFBP4 P22692;P22692-2 8 8 36,4 27,934 Insulin-like growth factor-binding protein 4 CA4 P22748;P22748-2 5 5 18,9 35,032 CPN2 P22792 9 9 19,4 60,556 Carboxypeptidase N subunit 2 PROZ P22891;P22891-2 7 7 28,8 44,743 Vitamin K-dependent MRC1 P22897;P22897-2 33 33 27,5 166,01 Macrophage 1 P23083 3 3 30,8 13,009 Ig heavy chain V-I region V35 FBLN1 P23142;P23142- 26 6 53,6 77,213 Fibulin-1 2;P23142- 3;CON__ENSEMBL:ENS BTAP00000016046

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FBLN1 P23142-4 28 8 58,9 74,433 Fibulin-1 ITGA6 P23229-7;P23229- 1 1 1,5 106,58 Integrin alpha-6;Integrin alpha-6 heavy 4;P23229-2;P23229- chain;Integrin alpha-6 light 5;P23229-3;P23229- chain;Processed integrin alpha-6 9;P23229-6;P23229 PPIB P23284 12 12 49,5 23,742 Peptidyl-prolyl cis-trans isomerase B S100A1 P23297 1 1 16 10,546 Protein S100-A1 GCSH P23434 2 2 17,3 18,884 Glycine cleavage system H protein, mitochondrial CBLN1 P23435 7 5 38,9 21,097 Cerebellin-1;Cerebellin;[des-Ser1]- cerebellin PTPRB P23467-4;P23467- 2 2 1,2 214,5 Receptor-type tyrosine-protein 2;P23467;P23467-3 phosphatase beta PTPRD P23468;P23468- 33 1 24,9 214,76 Receptor-type tyrosine-protein 7;P23468-5;P23468- phosphatase delta 6;P23468-3 PTPRD P23468-2 32 1 24,7 212,13 Receptor-type tyrosine-protein phosphatase delta PTPRD P23468-4 32 1 31,2 169,47 Receptor-type tyrosine-protein phosphatase delta PTPRG P23470-2;P23470 10 10 8,5 158,77 Receptor-type tyrosine-protein phosphatase gamma PTPRZ1 P23471- 29 29 14,3 253,67 Receptor-type tyrosine-protein 2;P23471;P23471-3 phosphatase zeta OMG P23515 8 8 22,7 49,607 -myelin glycoprotein AHCY P23526;P23526-2 5 5 14,1 47,716 Adenosylhomocysteinase CFL1 P23528 10 7 57,2 18,502 Cofilin-1 BDNF P23560;P23560- 2 2 15,4 27,818 Brain-derived neurotrophic factor 2;P23560-3;P23560- 5;P23560-4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] NPPC P23582 2 2 25,4 13,246 C-type natriuretic peptide;CNP- 22;CNP-29;CNP-53 ATP2B4;ATP2B1 P23634-7;P23634- 2 2 2,6 132,59 Plasma membrane calcium- 6;P23634- transporting ATPase 4;Plasma 8;P23634;P23634- membrane calcium-transporting 5;P23634-4;P23634- ATPase 1 3;P23634-2;P20020- 5;P20020-2;P20020- 6;P20020-3;P20020- 4;P20020 LAMA2 P24043 80 80 35,1 343,9 Laminin subunit alpha-2 CRHBP P24387 2 2 10,9 36,144 Corticotropin-releasing factor-binding protein IGFBP6 P24592 9 9 39,2 25,322 Insulin-like growth factor-binding protein 6 IGFBP5 P24593 9 9 48,5 30,57 Insulin-like growth factor-binding protein 5 ACP1 P24666-3;P24666- 3 3 35,5 14,342 Low molecular weight 2;P24666;P24666-4 phosphotyrosine protein phosphatase TNC P24821- 18 18 14,9 230,86 Tenascin 4;P24821;P24821- 5;P24821-2;P24821- 3;P24821-6 MPZ P25189;P25189-2 4 4 16,5 27,554 Myelin protein P0 AZGP1 P25311 20 20 55,4 34,258 Zinc-alpha-2-glycoprotein CTSS P25774;P25774-2 9 9 27,2 37,495 Cathepsin S MSN P26038 20 11 35,4 67,819 Moesin S100A4 P26447 2 2 18,8 11,728 Protein S100-A4 MGAT1 P26572 12 12 32,8 50,878 Alpha-1,3-mannosyl-glycoprotein 2- beta-N-acetylglucosaminyltransferase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CD27 P26842 1 1 5,4 29,137 CD27 antigen FKBP2 P26885 5 5 47,2 15,649 Peptidyl-prolyl cis-trans isomerase FKBP2 MST1 P26927;Q2TV78;Q2TV7 15 15 30,8 80,319 Hepatocyte growth factor-like 8-2 protein;Hepatocyte growth factor-like protein alpha chain;Hepatocyte growth factor-like protein beta chain CNTFR P26992 8 8 29 40,633 Ciliary neurotrophic factor receptor subunit alpha ACVR2A P27037 1 1 3,7 57,847 Activin receptor type-2A PON1 P27169 13 13 61,4 39,731 Serum / 1 YWHAQ P27348 5 2 23,7 27,764 14-3-3 protein theta CALR P27797 17 17 63,5 48,141 MAP4 P27816-5;P27816- 4 4 7 85,251 Microtubule-associated protein 4 2;P27816- 6;P27816;P27816- 7;P27816-4 CANX P27824;P27824- 9 9 19,8 67,567 2;P27824-3 CFP P27918 6 6 20,7 51,276 Properdin PSMB5 P28074;P28074- 2 2 11 28,48 Proteasome subunit beta type-5 3;P28074-2 MAPK1 P28482;P28482-2 3 3 10 41,389 Mitogen-activated protein kinase 1 GRN P28799;P28799- 10 10 20,9 63,544 Granulins;Acrogranin;Paragranulin;Gra 3;P28799-2 nulin-1;Granulin-2;Granulin- 3;Granulin-4;Granulin-5;Granulin- 6;Granulin-7 PTPRM P28827;P28827-2 12 12 13,3 163,68 Receptor-type tyrosine-protein phosphatase mu LAP3 P28838-2;P28838 3 3 8,4 52,771 aminopeptidase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TNFRSF8 P28908 2 2 5,5 63,747 Tumor necrosis factor receptor superfamily member 8 PCSK1 P29120-2;P29120 9 9 14,9 79,009 Neuroendocrine convertase 1 PCSK6 P29122-2;P29122- 4 4 6,4 105,12 / 8;P29122;P29122- type 6 7;P29122-3;P29122- 6;P29122-5;P29122-4

IMPA1 P29218;P29218- 11 11 44,8 30,188 Inositol monophosphatase 1 3;P29218-2 CTGF P29279-2;P29279 6 6 27 35,205 Connective tissue growth factor EPHB2 P29323-2;P29323- 6 6 9 109,87 Ephrin type-B receptor 2 3;P29323 CRABP2 P29373 2 2 16,7 15,693 Cellular retinoic acid-binding protein 2 TKT P29401;P29401-2 8 8 19,6 67,877 Transketolase SERPINA4 P29622 21 21 58,3 48,541 Kallistatin CRABP1 P29762 2 2 17,5 15,565 Cellular retinoic acid-binding protein 1 MARCKS P29966 5 5 32,5 31,554 Myristoylated alanine-rich C-kinase AQP1 P29972-4;P29972- 1 1 13 16,677 -1 2;P29972-3;P29972 PRDX6 P30041 13 13 65,6 25,035 Peroxiredoxin-6 BLVRB P30043 8 8 58,7 22,119 Flavin reductase (NADPH) PRDX5 P30044- 6 6 56,2 17,031 Peroxiredoxin-5, mitochondrial 2;P30044;P30044- 3;P30044-4 PRDX3 P30048-2;P30048 4 4 15,1 25,838 Thioredoxin-dependent peroxide reductase, mitochondrial CMPK1 P30085-2;P30085 2 2 11,6 16,548 UMP-CMP kinase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PEBP1 P30086 11 11 77 21,057 Phosphatidylethanolamine-binding protein 1;Hippocampal cholinergic neurostimulating peptide PDIA3 P30101 21 20 49,5 56,782 Protein disulfide-isomerase A3 HLA-B P30483;P30481 6 1 23,5 40,414 HLA class I histocompatibility antigen, B-45 alpha chain;HLA class I histocompatibility antigen, B-44 alpha chain HLA-A P30512;P30456 7 1 29 40,862 HLA class I histocompatibility antigen, A-29 alpha chain;HLA class I histocompatibility antigen, A-43 alpha chain AXL P30530-2;P30530 7 7 12,9 97,376 Tyrosine-protein kinase receptor UFO SLC6A1 P30531 1 1 3,5 67,073 Sodium- and chloride-dependent GABA transporter 1 LRPAP1 P30533 2 2 4,8 41,465 Alpha-2-macroglobulin receptor- associated protein PKLR P30613-2;P30613 3 2 7,4 58,494 Pyruvate kinase PKLR SRI P30626-3;P30626- 1 1 6,1 20,006 Sorcin 2;P30626 GSTT1 P30711-2;P30711 1 1 15,6 13,517 Glutathione S-transferase theta-1 SERPINB1 P30740;P30740-2 4 4 13,5 42,741 Leukocyte inhibitor CORO1A P31146 3 3 7,8 51,026 Coronin-1A GDI1 P31150 16 9 43 50,582 Rab GDP dissociation inhibitor alpha P31151;Q86SG5 4 4 41,6 11,471 Protein S100-A7 MAT2A P31153;P31153-2 3 3 8,1 43,66 S-adenosylmethionine synthase isoform type-2 PRKAR1B P31321 3 2 8,9 43,072 cAMP-dependent protein kinase type I-beta regulatory subunit SDC4 P31431-2;P31431 3 3 23,5 16,545 Syndecan-4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DNAJA1 P31689-2;P31689 2 2 7,6 37,044 DnaJ homolog subfamily A member 1 CASP14 P31944 2 2 12 27,679 Caspase-14;Caspase-14 subunit p19;Caspase-14 subunit p10 YWHAB P31946-2;P31946 9 5 47,5 27,85 14-3-3 protein beta/alpha;14-3-3 protein beta/alpha, N-terminally processed STIP1 P31948- 2 2 6,2 59,777 Stress-induced-phosphoprotein 1 3;P31948;P31948-2 S100A11 P31949 1 1 15,2 11,74 Protein S100-A11;Protein S100-A11, N- terminally processed L1CAM P32004-3;P32004- 26 26 28 138,91 Neural cell adhesion molecule L1 2;P32004 PRDX2 P32119;P32119-2 13 12 66,7 21,892 Peroxiredoxin-2 SLC8A1 P32418-2;P32418- 3 3 6,8 104,69 Sodium/calcium exchanger 1 3;P32418-4;P32418- 5;P32418 TNFSF8 P32971 2 2 9 26,017 Tumor necrosis factor ligand superfamily member 8 CDH5 P33151;P33151-2 5 5 7,4 87,527 Cadherin-5 LSP1 P33241- 1 1 9,7 30,213 Lymphocyte-specific protein 1 2;P33241;P33241-3 MAN1A1 P33908;P33908-2 16 15 30,5 72,968 Mannosyl-oligosaccharide 1,2-alpha- mannosidase IA GALNS P34059 6 6 16,1 58,025 N-acetylgalactosamine-6-sulfatase RNASE4 P34096 7 7 39,5 16,84 SDC2 P34741 2 2 7,5 22,16 Syndecan-2 BMP8B;BMP8A P34820- 2 2 8,9 39,151 Bone morphogenetic protein 8B;Bone 2;Q7Z5Y6;P34820 morphogenetic protein 8A HSPA4 P34932;P34932-2 3 3 5 94,33 Heat shock 70 kDa protein 4 GPC1 P35052;P35052-2 14 14 40 61,68 Glypican-1;Secreted glypican-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SERPINB6 P35237 9 9 34,8 42,621 Serpin B6 RDX P35241;P35241- 13 4 22,5 68,563 Radixin 5;P35241-4;P35241- 3;P35241-2 SFTPD P35247 1 1 4 37,728 Pulmonary surfactant-associated protein D ADM P35318 2 2 14,6 20,42 ADM;;Proadrenomedu llin N-20 terminal peptide THBS2 P35442 21 21 26,5 129,99 Thrombospondin-2 THBS4 P35443;P49746-2 17 14 31,2 105,87 Thrombospondin-4 IDUA P35475;P35475-2 5 5 10,4 72,669 Alpha-L-iduronidase SAA4 P35542 3 3 21,5 14,746 Serum amyloid A-4 protein FBN1 P35555 43 42 22,2 312,24 -1 FBN2 P35556;P35556-2 2 1 1 314,77 Fibrillin-2 MYH9 P35579;P35579- 10 6 5,6 226,53 Myosin-9 2;P35580;P35580- 5;P35580-2;P35580- 3;P35580-4 TIE1 P35590;P35590- 10 10 14,1 125,09 Tyrosine-protein kinase receptor Tie-1 3;P35590-2 ADD1 P35611-2;P35611- 3 3 4,8 69,984 Alpha-adducin 6;P35611- 4;P35611;P35611- 3;P35611-5 BSG P35613- 7 7 44,2 29,221 2;P35613;P35613- 4;P35613-3 TIMP3 P35625 2 2 11,4 24,145 Metalloproteinase inhibitor 3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MYH11 P35749-4;P35749- 8 4 4,7 223,57 Myosin-11 3;P35749;P35749- 2;Q7Z406;Q7Z406- 6;Q7Z406-2 GLRX P35754 3 3 42,5 11,776 Glutaredoxin-1 IGFALS P35858;P35858-2 16 16 33,2 66,034 Insulin-like growth factor-binding protein complex acid labile subunit FLT4 P35916-3;P35916- 2 2 3,3 93,173 Vascular endothelial growth factor 1;P35916 receptor 3 KDR P35968-2;P35968- 3 3 7,2 75,895 Vascular endothelial growth factor 3;P35968 receptor 2 CHI3L1 P36222 21 21 63,7 42,625 Chitinase-3-like protein 1 GGT5 P36269- 4 4 9,7 58,992 Gamma-glutamyltransferase 2;P36269;P36269-3 5;Gamma-glutamyltransferase 5 heavy chain;Gamma-glutamyltransferase 5 light chain PGM1 P36871;P36871- 12 12 23,7 61,448 Phosphoglucomutase-1 2;P36871-3 ACVR1B P36896-5;P36896- 3 3 7,3 51,724 Activin receptor type-1B 2;P36896- 3;P36896;P36896-4 SERPINF1 P36955 26 21 65,3 46,312 Pigment epithelium-derived factor DLST P36957;P36957-2 3 3 7,1 48,755 Dihydrolipoyllysine-residue succinyltransferase component of 2- oxoglutarate dehydrogenase complex, mitochondrial CFHR2 P36980-2;P36980 6 4 28,8 27,896 Complement factor H-related protein 2 TGFBR2 P37173;P37173-2 1 1 2,6 64,567 TGF-beta receptor type-2 TAGLN2 P37802;P37802-2 3 3 18,1 22,391 Transgelin-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TALDO1 P37837 10 10 32 37,54 Transaldolase SNCA P37840- 3 3 43,8 11,372 Alpha-synuclein 2;P37840;P37840-3 LIPA P38571-2;P38571 2 2 7,9 39,111 Lysosomal acid lipase/cholesteryl ester hydrolase ATP6V1A P38606-2;P38606 1 1 3,1 64,735 V-type proton ATPase catalytic subunit A COL15A1 P39059 8 8 7,3 141,72 Collagen alpha-1(XV) chain;Restin;Restin-2;Restin-3;Restin-4 COL18A1 P39060-2;P39060- 16 16 14,8 135,76 Collagen alpha-1(XVIII) 1;P39060 chain;Endostatin CAPG P40121;P40121-2 5 5 21,3 38,498 Macrophage-capping protein CAP2 P40123-2;P40123 1 1 4,4 45,245 Adenylyl cyclase-associated protein 2 IL6ST P40189;P40189- 22 22 26,6 103,54 Interleukin-6 receptor subunit beta 3;P40189-2 MDH1 P40925;P40925- 15 15 44,9 36,426 , cytoplasmic 3;P40925-2 MDH2 P40926;P40926-2 13 13 50,9 35,503 Malate dehydrogenase, mitochondrial LEP P41159 2 2 18,6 18,64 Leptin CD200 P41217- 5 5 27,1 30,331 OX-2 membrane glycoprotein 2;P41217;P41217-3 PRPH P41219;P41219-2 2 1 4,5 53,65 PTGDS P41222 17 17 76,8 21,029 Prostaglandin-H2 D-isomerase NBL1 P41271;P41271-2 2 2 9,9 19,408 Neuroblastoma suppressor of tumorigenicity 1 GRIA1 P42261-3;P42261- 1 1 1,6 92,171 Glutamate receptor 1 4;P42261- 2;P42261;P42261- 6;P42261-5

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GRIA2 P42262-4;P42262- 4 4 6,1 93,774 Glutamate receptor 2 2;P42262;P42262-3 DPP6 P42658-2;P42658 10 9 16,8 91,34 Dipeptidyl aminopeptidase-like protein 6 PRCP P42785;P42785-2 13 13 30,2 55,799 Lysosomal Pro-X carboxypeptidase NSG1 P42857-2;P42857 5 5 45,2 16,467 -specific member 1 SLC1A3 P43003-2;P43003 2 2 7,2 55,148 Excitatory transporter 1 SLC1A2 P43004-3;P43004- 1 1 2,1 61,007 Excitatory amino acid transporter 2 2;P43004 PAFAH1B1 P43034 3 3 3,4 46,637 Platelet-activating factor acetylhydrolase IB subunit alpha MCAM P43121;P43121-2 24 24 42,3 71,607 Cell surface glycoprotein MUC18 DCC P43146 23 23 24,8 158,45 Netrin receptor DCC CTSO P43234 4 4 18,4 35,957 Cathepsin O BTD P43251- 15 15 37,1 58,913 Biotinidase 4;P43251;P43251- 3;P43251-2 RANBP1 P43487-2;P43487 1 1 5,5 23,239 -specific GTPase-activating protein AFM P43652 31 30 52,9 69,068 Afamin PPIC P45877 4 4 29,2 22,763 Peptidyl-prolyl cis-trans isomerase C CRK P46108-2;P46108 2 2 13,7 22,905 Adapter molecule crk CRKL P46109 1 1 3 33,777 Crk-like protein NSF P46459;P46459-2 5 5 8,3 82,593 Vesicle-fusing ATPase NOTCH1 P46531 6 6 4,6 272,5 Neurogenic notch homolog protein 1; extracellular truncation;Notch 1 intracellular domain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MAP1B P46821 3 3 2,1 270,63 Microtubule-associated protein 1B;MAP1B heavy chain;MAP1 light chain LC1 GNPDA1 P46926;P46926-2 2 1 7,6 32,668 Glucosamine-6-phosphate isomerase 1 YAP1 P46937-5;P46937- 1 1 4 48,274 Yorkie homolog 3;P46937-6;P46937- 7;P46937-2;P46937- 8;P46937;P46937-9 GYG1 P46976-3;P46976- 1 1 3,6 31,466 -1 2;P46976 CAPZB P47756-2;P47756 4 4 12,1 30,628 F-actin-capping protein subunit beta NPTX2 P47972 10 10 31,6 47,041 Neuronal pentraxin-2 GRIA4 P48058-2;P48058 15 15 33 49,146 Glutamate receptor 4 CXCL12 P48061-2;P48061- 2 2 24,7 10,103 Stromal cell-derived factor 1;SDF-1- 5;P48061;P48061- beta(3-72);SDF-1-alpha(3-67) 6;P48061-3;P48061-4

PREP P48147 11 11 21,5 80,699 Prolyl ME1 P48163;P48163-2 4 4 10 64,149 NADP-dependent malic enzyme PCP4 P48539 3 3 43,5 6,7913 Purkinje cell protein 4 IFNAR2 P48551-3;P48551- 2 2 13,8 27,384 Interferon alpha/beta receptor 2 2;P48551 GSS P48637;P48637-2 7 7 20,7 52,384 Glutathione synthetase HSPA13 P48723 15 15 33,8 51,927 Heat shock 70 kDa protein 13 MASP1 P48740 17 3 34,6 79,246 Mannan-binding lectin serine protease 1;Mannan-binding lectin serine protease 1 heavy chain;Mannan- binding lectin serine protease 1 light chain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MASP1 P48740-2;P48740-4 21 7 40,1 81,859 Mannan-binding lectin serine protease 1;Mannan-binding lectin serine protease 1 heavy chain;Mannan- binding lectin serine protease 1 light chain MASP1 P48740-3 14 2 48,7 43,639 Mannan-binding lectin serine protease 1;Mannan-binding lectin serine protease 1 heavy chain;Mannan- binding lectin serine protease 1 light chain NOV P48745 13 13 50,1 39,162 Protein NOV homolog CD97 P48960-2;P48960- 3 3 6,3 81,742 CD97 antigen;CD97 antigen subunit 3;P48960 alpha;CD97 antigen subunit beta DNASE1L1 P49184 4 4 23,2 33,892 Deoxyribonuclease-1-like 1 ALDH9A1 P49189-2;P49189 2 2 5,7 46,454 4-trimethylaminobutyraldehyde dehydrogenase LMAN1 P49257 7 7 17,6 57,548 Protein ERGIC-53 TUFM P49411 1 1 3,3 49,541 Elongation factor Tu, mitochondrial AMPH P49418;P49418-2 7 7 18,4 76,256 Amphiphysin AARS P49588;P49588-2 3 3 3,9 106,81 Alanine--tRNA ligase, cytoplasmic CARS P49589;P49589-3 1 1 1,9 85,472 Cysteine--tRNA ligase, cytoplasmic MAN2A2 P49641;P49641- 35 34 39,4 130,54 Alpha-mannosidase 2x 1;P49641-2 PSMB2 P49721 1 1 5 22,836 Proteasome subunit beta type-2 THBS3 P49746 2 1 4 104,2 Thrombospondin-3 COMP P49747;P49747- 15 13 35,4 82,86 Cartilage oligomeric matrix protein 2;CON__ENSEMBL:ENS BTAP00000006074

VEGFC P49767 3 3 10,5 46,883 Vascular endothelial growth factor C

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HINT1 P49773 2 2 27 13,802 Histidine triad nucleotide-binding protein 1 FHIT P49789 1 1 6,8 16,858 Bis(5-adenosyl)- KLK7 P49862;P49862-2 3 3 13,4 27,524 Kallikrein-7 SEPP1 P49908 6 6 18,1 43,173 Selenoprotein P ENTPD1 P49961-3;P49961- 1 1 4,6 34,174 Ectonucleoside triphosphate 4;P49961- diphosphohydrolase 1 5;P49961;P49961- 2;P49961-6 MMP14 P50281 2 2 4 65,893 -14 GDI2 P50395;P50395-2 18 11 45,8 50,663 Rab GDP dissociation inhibitor beta ST13;ST13P4;ST13P5 P50502;Q8IZP2;Q8NFI4 5 5 15,2 41,331 Hsc70-interacting protein;Putative protein FAM10A4;Putative protein FAM10A5 BCAM P50895 13 13 29,8 67,404 Basal cell adhesion molecule PPT1 P50897;P50897-2 2 2 9,5 34,193 Palmitoyl-protein 1 CCT8 P50990- 2 2 5,1 57,645 T-complex protein 1 subunit theta 2;P50990;P50990-3 ATP1A2 P50993 6 3 8,5 112,26 Sodium/potassium-transporting ATPase subunit alpha-2 RAB7A P51149 1 1 6,8 23,489 Ras-related protein Rab-7a FABP6 P51161;P51161-2 1 1 8,6 14,371 Gastrotropin MMP15 P51511 4 4 7,5 75,806 Matrix metalloproteinase-15 MMP16 P51512;P51512-2 3 3 5,4 69,521 Matrix metalloproteinase-16 APLP1 P51693 22 2 43,2 72,176 Amyloid-like protein 1;C30 APLP1 P51693-2 22 2 43,3 72,247 Amyloid-like protein 1;C30 PLXNA3 P51805 1 1 1,2 207,7 Plexin-A3 LUM P51884 13 8 40,2 38,429 PRELP P51888 9 9 30,6 43,809 Prolargin

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PGD P52209-2;P52209 6 6 17 51,872 6-phosphogluconate dehydrogenase, decarboxylating ARHGDIA P52565;P52565-2 3 3 15,7 23,207 Rho GDP-dissociation inhibitor 1 ARHGDIB P52566 4 4 33,8 22,988 Rho GDP-dissociation inhibitor 2 HRSP12 P52758 4 4 45,3 14,494 Ribonuclease UK114 EFNA3 P52797 1 1 6,7 26,35 Ephrin-A3 EFNB2 P52799 7 7 21 36,923 Ephrin-B2 EFNA5 P52803 1 1 8,3 26,297 Ephrin-A5 STC1 P52823-2;P52823 3 3 21,9 20,487 Stanniocalcin-1 NDST1 P52848;P52848- 12 11 16,4 100,87 Bifunctional N- 2;Q9H3R1;P52849- deacetylase/N-sulfotransferase 2;O95803-2;O95803- 1;Heparan sulfate N-deacetylase 3;O95803 1;Heparan sulfate N-sulfotransferase 1

NDST2 P52849 2 1 2,8 100,87 Bifunctional heparan sulfate N- deacetylase/N-sulfotransferase 2;Heparan sulfate N-deacetylase 2;Heparan sulfate N-sulfotransferase 2 THOP1 P52888;P52888-2 2 2 2,5 78,839 Thimet AKR1C1;AKR1C2 Q04828;P52895 1 1 7,1 36,788 Aldo-keto reductase family 1 member C1;Aldo-keto reductase family 1 member C2 CAPZA1;CAPZA2 P52907;P47755- 2 2 10,5 32,922 F-actin-capping protein subunit alpha- 2;P47755 1;F-actin-capping protein subunit alpha-2 CRIP2 P52943;P52943-2 3 3 32,2 22,492 Cysteine-rich protein 2 PPP5C P53041 3 3 9,8 56,878 Serine/threonine-protein phosphatase 5

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CTSC P53634;P53634- 14 14 39,1 51,853 1;Dipeptidyl 2;P53634-3 peptidase 1 exclusion domain chain;Dipeptidyl peptidase 1 heavy chain;Dipeptidyl peptidase 1 light chain PTTG1IP P53801 1 1 10 20,324 Pituitary tumor-transforming gene 1 protein-interacting protein CACNA2D1 P54289-2;P54289- 39 1 43,6 123,18 Voltage-dependent 5;P54289 subunit alpha-2/delta-1;Voltage- dependent calcium channel subunit alpha-2-1;Voltage-dependent calcium channel subunit delta-1 CACNA2D1 P54289-3;P54289-4 39 1 43,6 122,63 Voltage-dependent calcium channel subunit alpha-2/delta-1;Voltage- dependent calcium channel subunit alpha-2-1;Voltage-dependent calcium channel subunit delta-1 USP14 P54578-2;P54578- 3 3 9,8 52,385 Ubiquitin carboxyl-terminal hydrolase 3;P54578 14 HSPA2 P54652 6 2 11,1 70,02 Heat shock-related 70 kDa protein 2 BCAT1 P54687- 2 2 9,5 38,645 Branched-chain-amino-acid 3;P54687;P54687- aminotransferase, cytosolic 2;P54687-4;P54687-5

ATP1B3 P54709-2;P54709 1 1 7,8 21,713 Sodium/potassium-transporting ATPase subunit beta-3 RAD23B P54727;P54727-2 5 3 16,9 43,171 UV excision repair protein RAD23 homolog B EPHB3 P54753 2 2 2,7 110,33 Ephrin type-B receptor 3 EPHA5 P54756- 7 5 9,7 112,62 Ephrin type-A receptor 5 2;P54756;P54756-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] EPHB4 P54760-4;P54760- 2 2 8,9 45,195 Ephrin type-B receptor 4 2;P54760;P54760-3 EPHA4 P54764;P54764-2 17 16 27,6 109,86 Ephrin type-A receptor 4 NAGLU P54802 13 13 25,3 82,265 Alpha-N-acetylglucosaminidase;Alpha- N-acetylglucosaminidase 82 kDa form;Alpha-N-acetylglucosaminidase 77 kDa form GALC P54803;P54803- 5 5 10,1 77,032 Galactocerebrosidase 4;P54803-5;P54803-3

GAS1 P54826 3 3 18,6 35,693 Growth arrest-specific protein 1 NAPA P54920 4 3 16,9 33,232 Alpha-soluble NSF attachment protein MFAP2 P55001-3;P55001- 1 1 12,4 17,444 Microfibrillar-associated protein 2 2;P55001 AIF1 P55008;P55008- 2 2 20,4 16,703 Allograft inflammatory factor 1 2;P55008-3 SLC12A2 P55011-3;P55011 7 7 10,5 129,68 12 member 2 PLTP P55058;P55058- 16 16 38,5 54,739 transfer protein 4;P55058-3;P55058-2

VCP P55072 9 9 15,6 89,321 Transitional ATPase MFAP4 P55083;P55083-2 2 2 9,8 28,648 Microfibril-associated glycoprotein 4 AQP4 P55087-2;P55087 2 2 8,6 32,299 Aquaporin-4 INHBC P55103 2 2 7,7 38,237 Inhibin beta C chain MANF P55145 1 1 7,7 20,7 Mesencephalic astrocyte-derived neurotrophic factor LAMB2 P55268 31 31 25,6 195,98 Laminin subunit beta-2 CDH4 P55283;P55283-2 5 5 9,5 100,28 Cadherin-4 CDH6 P55285-2;P55285 12 11 24,6 73,863 Cadherin-6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CDH8 P55286 7 7 14,3 88,252 Cadherin-8 CDH11 P55287-2;P55287 13 13 29,3 76,456 Cadherin-11 CDH12 P55289-2;P55289 7 7 12,3 83,999 Cadherin-12 CDH13 P55290;P55290- 14 14 26,4 78,286 Cadherin-13 4;P55290-5;P55290- 3;P55290-2 CDH15 P55291 20 20 34,6 88,915 Cadherin-15 TPD52 P55327-8;P55327- 1 1 9,9 16,853 Tumor protein D52 2;P55327- 4;P55327;P55327- 7;P55327-5;P55327- 6;P55327-3 CCL18 P55774 2 2 24,7 9,8487 C-C motif chemokine 18;CCL18(1- 68);CCL18(3-69);CCL18(4-69) NPEPPS P55786;P55786- 26 26 37,2 103,28 Puromycin-sensitive aminopeptidase 2;A6NEC2;A6NEC2- 2;A6NEC2-3 SUMO2;SUMO4;SUMO3 P61956- 1 1 16,9 8,1111 Small ubiquitin-related modifier 2;Q6EEV6;P61956;P558 2;Small ubiquitin-related modifier 54;P55854-2 4;Small ubiquitin-related modifier 3 FCGRT P55899 2 2 6,6 39,743 IgG receptor FcRn subunit p51 GFRA1 P56159-2;P56159 3 3 9,3 50,838 GDNF family receptor alpha-1 ITGA1 P56199 1 1 1 130,85 Integrin alpha-1 WNT4 P56705 1 1 4,3 39,051 Protein Wnt-4 BACE1 P56817-4;P56817- 3 3 10,4 48,159 Beta-secretase 1 3;P56817- 2;P56817;P56817- 6;P56817-5 NRG3 P56975-4;P56975- 3 3 5 75,03 Pro--3, membrane-bound 2;P56975;P56975-3 isoform;Neuregulin-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] JAM2 P57087;P57087- 6 6 27,2 33,207 Junctional adhesion molecule B 3;P57087-2 LOXL3 P58215;P58215- 6 6 14,3 83,166 Lysyl oxidase homolog 3 3;P58215-2 ANTXR2 P58335-2;P58335- 3 3 8,8 42,892 Anthrax toxin receptor 2 4;P58335;P58335-3 NRXN1 P58400 9 1 29,6 46,86 -1-beta NRXN2 P58401 7 1 11,6 70,926 Neurexin-2-beta NXPH1 P58417 5 4 20,3 31,082 Neurexophilin-1 FAM3B P58499- 3 3 23,5 20,814 Protein FAM3B 3;P58499;P58499-2 MTPN P58546 2 2 25,4 12,895 Myotrophin DEFB1 P60022 1 1 33,8 7,4197 Beta-defensin 1 CD81 P60033 2 2 18,2 25,809 CD81 antigen TPI1 P60174- 13 13 72,3 26,669 Triosephosphate isomerase 1;P60174;P60174-4 GABARAPL2 P60520 6 4 40,2 13,667 Gamma-aminobutyric acid receptor- associated protein-like 2 MYL6 P60660- 4 4 34,4 16,961 Myosin light polypeptide 6 2;P60660;P14649 ACTG1;ACTB P63261;P60709;Q6S8J3 18 7 57,9 41,792 Actin, cytoplasmic 2;Actin, cytoplasmic ;A5A3E0;P0CG38;Q9BY 2, N-terminally processed;Actin, X7;P0CG39 cytoplasmic 1;Actin, cytoplasmic 1, N- terminally processed PRPS1 P60891 2 1 11,3 34,834 Ribose-phosphate pyrophosphokinase 1 PSMA6 P60900;P60900-2 3 3 13,8 27,399 Proteasome subunit alpha type-6 CDC42 P60953 1 1 8,9 21,258 Cell division control protein 42 homolog DSTN P60981-2;P60981 3 3 14,9 16,62

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GMFB P60983;O60234 6 6 44,4 16,713 beta RAB4B P61018;P61018-2 2 2 7,5 23,586 Ras-related protein Rab-4B RAB2A P61019-2;P61019 1 1 7,4 20,847 Ras-related protein Rab-2A UBE2D2;UBE2D3 P62837- 1 1 9,3 13,635 Ubiquitin-conjugating enzyme E2 2;P62837;P61077;P610 D2;Ubiquitin-conjugating enzyme E2 77-2;P61077-3 D3 UBE2N P61088;Q5JXB2 4 4 22,4 17,138 Ubiquitin-conjugating enzyme E2 N RAB14 P61106 3 3 27,4 23,897 Ras-related protein Rab-14 ACTR3 P61158 3 3 11,2 47,371 Actin-related protein 3 ACTR2 P61160;P61160-2 2 2 6,3 44,76 Actin-related protein 2 ARF1;ARF3 P84077;P61204;P6120 3 3 21,5 20,697 ADP-ribosylation factor 1;ADP- 4-2;P84085 ribosylation factor 3 STX1B P61266-2;P61266 4 4 15,9 31,786 Syntaxin-1B SST P61278 1 1 28,4 12,735 ;Somatostatin- 28;Somatostatin-14 HSPE1 P61604 5 5 52 10,932 10 kDa heat shock protein, mitochondrial LYZ P61626 3 3 35,1 16,537 Lysozyme C B2M P61769 6 6 57,1 13,714 Beta-2-microglobulin;Beta-2- microglobulin form pI 5.3 TGFB2 P61812;P61812-2 4 4 10,1 47,747 Transforming growth factor beta- 2;Latency-associated peptide NPC2 P61916;P61916-2 13 13 80,1 16,57 Epididymal secretory protein E1 UFM1 P61960 1 1 17,6 9,1175 Ubiquitin-fold modifier 1 NUTF2 P61970 5 5 69,3 14,478 Nuclear transport factor 2 HNRNPK P61978- 1 1 2 48,562 Heterogeneous nuclear 3;P61978;P61978-2 ribonucleoprotein K YWHAG P61981 5 2 22,7 28,302 14-3-3 protein gamma;14-3-3 protein gamma, N-terminally processed

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CALM1 P62158;P27482 5 5 45,6 16,837 YWHAE P62258;P62258-2 15 13 63,9 29,174 14-3-3 protein epsilon TMSB4X P62328 2 2 43,2 5,0526 Thymosin beta-4;Hematopoietic system regulatory peptide VSNL1 P62760 4 4 15,7 22,142 Visinin-like protein 1 HIST1H4A P62805 3 3 29,1 11,367 Histone H4 RAB1A;RAB1B;RAB1C;RA P62820- 2 2 19,1 15,33 Ras-related protein Rab-1A;Ras-related B10;RAB13;RAB8B;RAB8 2;Q9H0U4;Q92928;P62 protein Rab-1B;Putative Ras-related A;RAB15 820;P62820- protein Rab-1C;Ras-related protein 3;P61026;P51153;Q929 Rab-10;Ras-related protein Rab- 30;P61006- 13;Ras-related protein Rab-8B;Ras- 2;P61006;P59190- related protein Rab-8A;Ras-related 2;P59190 protein Rab-15 RAN P62826 3 3 14,8 24,423 GTP-binding nuclear protein Ran RPS28 P62857 1 1 17,4 7,8409 40S ribosomal protein S28 PPIA P62937;P62937- 9 9 49,1 18,012 Peptidyl-prolyl cis-trans isomerase 2;P0DN26;A0A0B4J2A2 A;Peptidyl-prolyl cis-trans isomerase A, ;A0A075B759;Q9Y536; N-terminally processed F5H284 FKBP1A P62942 2 2 25 11,951 Peptidyl-prolyl cis-trans isomerase FKBP1A GRB2 P62993;P62993-2 8 8 46,5 25,206 Growth factor receptor-bound protein 2 AP2B1 P63010- 12 9 13,8 98,117 AP-2 complex subunit beta 3;P63010;P63010-2 VAMP2 P63027 1 1 13,8 12,663 Vesicle-associated membrane protein 2 PPP3R1 P63098 1 1 5,9 19,3 subunit B type 1 YWHAZ P63104;P63104-2 12 9 53,9 27,745 14-3-3 protein zeta/delta SKP1 P63208;P63208-2 6 6 52,1 18,658 S-phase kinase-associated protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] EIF5A;EIF5A2;EIF5AL1 P63241;P63241- 2 2 15,6 16,832 Eukaryotic initiation factor 2;Q9GZV4;Q6IS14 5A-1;Eukaryotic translation initiation factor 5A-2;Eukaryotic translation initiation factor 5A-1-like TPM4 P67936;P67936-2 5 2 23,8 28,521 Tropomyosin alpha-4 chain ACTA1;ACTC1;ACTG2;AC P68133;P68032;P6326 13 2 35,8 42,051 Actin, alpha skeletal muscle;Actin, TA2 7;P62736;P63267-2 alpha cardiac muscle 1;Actin, gamma- enteric smooth muscle;Actin, aortic smooth muscle UBE2L3 P68036- 1 1 14,8 14,121 Ubiquitin-conjugating enzyme E2 L3 2;P68036;P68036-3 EEF1A1;EEF1A1P5;EEF1A P68104;P68104- 4 4 14,9 50,14 Elongation factor 1-alpha 1;Putative 2 2;Q5VTE0;Q05639 elongation factor 1-alpha-like 3;Elongation factor 1-alpha 2 TUBA1B;TUBA1A;TUBA1 P68363-2;Q71U36- 5 3 22,4 37,217 Tubulin alpha-1B chain;Tubulin alpha- C;TUBA3C;TUBA3E 2;Q9BQE3;Q71U36;P68 1A chain;Tubulin alpha-1C 363;Q13748- chain;Tubulin alpha-3C/D 2;Q6PEY2;Q13748;Q9N chain;Tubulin alpha-3E chain Y65-2;P68366- 2;P68366 TUBB4B;TUBB8;TUBB4A; P68371;Q3ZCM7;P043 2 2 6,1 49,83 Tubulin beta-4B chain;Tubulin beta-8 TUBB;TUBB2B;TUBB2A 50;P07437;Q9BVA1;Q1 chain;Tubulin beta-4A chain;Tubulin 3885 beta chain;Tubulin beta-2B chain;Tubulin beta-2A chain HBB P68871 16 9 96,6 15,998 ;LVV- -7; NOMO2;NOMO1;NOMO Q5JPE7- 11 11 13,3 134,19 Nodal modulator 2;Nodal modulator 3 2;Q15155;P69849;Q5JP 1;Nodal modulator 3 E7;Q5JPE7-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HBG2;HBG1 P69892;P69891 5 4 41,5 16,126 Hemoglobin subunit gamma- 2;Hemoglobin subunit gamma-1 HBA1 P69905;CON__P01966 14 13 78,2 15,257

CXADR P78310-5;P78310- 6 6 32,1 28,201 Coxsackievirus and adenovirus 7;P78310-2;P78310- receptor 6;P78310;P78310- 4;P78310-3 SIRPA;SIRPB1 P78324;P78324- 14 12 43,5 54,966 Tyrosine-protein phosphatase non- 4;P78324- receptor type substrate 1;Signal- 2;Q5TFQ8;Q9P1W8- regulatory protein beta-1 isoform 3 3;O00241-2;Q9P1W8- 4;Q9P1W8-2;Q9P1W8

GPC5 P78333 2 2 4 63,706 Glypican-5;Secreted glypican-5 CNTNAP1 P78357 2 2 1,5 156,26 Contactin-associated protein 1 OLR1 P78380;P78380- 2 2 12,5 30,959 Oxidized low-density lipoprotein 2;P78380-3 receptor 1;Oxidized low-density lipoprotein receptor 1, soluble form BTN3A2;BTN3A1;BTN3A P78410-3;P78410- 2 2 9,6 32,016 Butyrophilin subfamily 3 member 3 2;P78410;O00481- A2;Butyrophilin subfamily 3 member 2;O00481-3;O00481- A1;Butyrophilin subfamily 3 member 4;O00481;O00478- A3 2;O00478

GSTO1 P78417;P78417- 10 10 37,8 27,566 Glutathione S-transferase omega-1 3;P78417-2 JAG1 P78504;P78504-2 11 11 14,3 133,8 Protein jagged-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] RELN P78509-3;P78509- 74 74 32,4 384,09 2;P78509 ADAM17 P78536-2;P78536 4 4 8,6 78,542 Disintegrin and metalloproteinase domain-containing protein 17 SRPX P78539-4;P78539- 5 5 16,1 41,75 Sushi repeat-containing protein SRPX 5;P78539- 2;P78539;P78539-3 IL13RA1 P78552-2;P78552 1 1 4,7 31,658 Interleukin-13 receptor subunit alpha- 1 MAP1A P78559;P78559-2 3 3 2,2 305,48 Microtubule-associated protein 1A;MAP1A heavy chain;MAP1 light chain LC2 GPLD1 P80108;P80108-2 16 16 24,2 92,335 Phosphatidylinositol--specific D LCN2 P80188-2;P80188 3 3 22,2 22,457 Neutrophil -associated NUCB2 P80303-2;P80303 12 12 36,4 50,2 Nucleobindin-2;Nesfatin-1 ABAT P80404 1 1 3,8 56,438 4-aminobutyrate aminotransferase, mitochondrial P80419 4 4 38,1 13,087 Ig heavy chain V-III region GAR P80422 2 2 14,4 11,787 Ig gamma lambda chain V-II region DOT BASP1 P80723;P80723-2 6 6 51,5 22,693 Brain acid soluble protein 1 P80748 3 3 37,8 11,935 Ig lambda chain V-III region LOI DCD P81605;P81605-2 2 2 22,7 11,284 Dermcidin;Survival-promoting peptide;DCD-1 ADAMTSL3 P82987-2;P82987 7 7 6,7 187,24 ADAMTS-like protein 3 P83593 3 1 35,8 12,06 Ig kappa chain V-IV region STH MXRA7 P84157;P84157-2 4 2 27,5 21,466 Matrix-remodeling-associated protein 7

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MXRA7 P84157-3 3 1 22 18,207 Matrix-remodeling-associated protein 7 FBLN2 P98095-2;P98095 19 19 27,5 131,86 Fibulin-2 DGCR2 P98153-3;P98153- 4 4 19,9 36,713 Integral membrane protein 2;P98153 DGCR2/IDD VLDLR P98155-2;P98155 8 8 12,4 93,382 Very low-density lipoprotein receptor HSPG2 P98160 83 83 31,1 468,83 Basement membrane-specific heparan sulfate proteoglycan core protein;Endorepellin;LG3 peptide PKD1 P98161-2;P98161- 1 1 0,4 461,36 Polycystin-1 3;P98161 LRP2 P98164 3 3 0,7 521,95 Low-density lipoprotein receptor- related protein 2 EFNB1 P98172 5 5 24,9 38,006 Ephrin-B1 FAM3A P98173- 4 4 32,3 21,164 Protein FAM3A 3;P98173;P98173-2 ATP8B2 P98198-4;P98198- 1 1 4,4 44,213 Phospholipid-transporting ATPase ID 2;P98198;P98198-3 CYCS P99999;CON__P62894 5 5 39 11,749 c

PITPNA Q00169 4 4 20 31,806 Phosphatidylinositol transfer protein alpha isoform B4GALNT1 Q00973;Q00973- 9 9 25,1 58,882 Beta-1,4 N- 2;Q00973-3 acetylgalactosaminyltransferase 1 SPTBN1 Q01082 4 4 2,5 274,61 Spectrin beta chain, non-erythrocytic 1 CTBS Q01459 11 11 41,8 43,759 Di-N-acetylchitobiase FABP5 Q01469;A8MUU1 6 6 57 15,164 Fatty acid-binding protein, epidermal CAP1 Q01518-2;Q01518 3 3 8,2 51,83 Adenylyl cyclase-associated protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ATP2B2 Q01814-6;Q01814- 2 2 3,9 132,59 Plasma membrane calcium- 8;Q01814- transporting ATPase 2 5;Q01814;Q01814- 4;Q01814-7;Q01814- 3;Q01814-2

ROR1 Q01973-3;Q01973 3 3 12 43,825 Tyrosine-protein kinase transmembrane receptor ROR1 TAGLN Q01995 10 10 46,3 22,611 Transgelin CNTN2 Q02246 36 36 48,7 113,39 Contactin-2 DSC2 Q02487-2;Q02487 14 14 23,7 93,768 -2 FKBP4 Q02790 3 3 10,2 51,804 Peptidyl-prolyl cis-trans isomerase FKBP4;Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed PLOD1 Q02809;Q02809-2 20 20 35,8 83,549 Procollagen-lysine,2-oxoglutarate 5- dioxygenase 1 NUCB1 Q02818 28 28 66,8 53,879 Nucleobindin-1 AKAP12 Q02952-3;Q02952- 11 11 14,3 180,99 A-kinase anchor protein 12 2;Q02952 TGFBR3 Q03167-2;Q03167 13 13 19,4 93,427 Transforming growth factor beta receptor type 3 PLAUR Q03405;Q03405- 6 6 30,1 36,978 2;Q03405-3 surface receptor CFHR1 Q03591 9 2 30,9 37,65 Complement factor H-related protein 1 NOTCH2 Q04721;Q7Z3S9-2 12 10 7,5 265,4 Neurogenic locus notch homolog protein 2;Notch 2 extracellular truncation;Notch 2 intracellular domain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HGFAC Q04756;CON__ENSEM 11 11 26,4 70,681 Hepatocyte growth factor BL:ENSBTAP000000230 activator;Hepatocyte growth factor 55 activator short chain;Hepatocyte growth factor activator long chain GLO1 Q04760-2;Q04760 3 3 20,7 19,043 Lactoylglutathione lyase YWHAH Q04917 3 1 13 28,218 14-3-3 protein eta DNM1 Q05193-5;Q05193- 3 3 4 95,894 -1 3;Q05193- 2;Q05193;Q9UQ16- 5;Q9UQ16-2;Q9UQ16- 3;Q9UQ16;Q9UQ16-4

COL14A1 Q05707- 25 25 19,9 191,9 Collagen alpha-1(XIV) chain 2;Q05707;Q05707-3

ZP2 Q05996-2;Q05996 10 10 14,9 81,299 Zona pellucida sperm-binding protein 2;Processed zona pellucida sperm- binding protein 2 ITIH3 Q06033- 17 17 23,8 99,326 Inter-alpha-trypsin inhibitor heavy 2;Q06033;CON__Q0V8 chain H3 M9 TYRO3 Q06418 8 8 20,3 96,904 Tyrosine-protein kinase receptor TYRO3 APLP2 Q06481;Q06481- 23 21 38,4 86,955 Amyloid-like protein 2 3;Q06481-6;Q06481- 2;Q06481-4;Q06481-5

FMOD Q06828 9 9 36,7 43,178

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PRDX1 Q06830 10 8 53,8 22,11 Peroxiredoxin-1 C1QBP Q07021 1 1 5 31,362 Complement component 1 Q subcomponent-binding protein, mitochondrial ENPEP Q07075 1 1 1,3 109,24 COL16A1 Q07092-2;Q07092 5 5 5,4 157,56 Collagen alpha-1(XVI) chain DPT Q07507 3 3 17,9 24,005 Dermatopontin SCN1B Q07699;Q07699-2 2 2 14,2 24,707 subunit beta-1 LRP1 Q07954;Q07954-2 68 68 20,1 504,6 Prolow-density lipoprotein receptor- related protein 1;Low-density lipoprotein receptor-related protein 1 85 kDa subunit;Low-density lipoprotein receptor-related protein 1 515 kDa subunit;Low-density lipoprotein receptor-related protein 1 intracellular domain PCDH1 Q08174-2;Q08174 15 15 16,4 133,72 Protocadherin-1 PPP3CA Q08209- 3 3 15,6 31,736 Serine/threonine-protein phosphatase 4;Q08209;Q08209- 2B catalytic subunit alpha isoform 5;Q08209-3;Q08209-2

DDR1 Q08345-2;Q08345- 10 10 13,1 97,173 Epithelial discoidin domain-containing 6;Q08345;Q08345- receptor 1 5;Q08345-4 GOLGA3 Q08378;Q08378- 2 2 2,7 167,35 Golgin subfamily A member 3 4;Q08378-2 LGALS3BP Q08380 14 14 34,9 65,33 Galectin-3-binding protein LOXL1 Q08397 3 3 8,7 63,109 Lysyl oxidase homolog 1 MFGE8 Q08431;Q08431- 12 12 32,8 43,122 Lactadherin;Lactadherin short 2;Q08431-3 form;Medin

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DSC1 Q08554-2;Q08554 5 5 8,3 93,834 Desmocollin-1 SPOCK1 Q08629 19 17 54,7 49,124 Testican-1 SIGLEC14;SIGLEC5 Q08ET2;O15389 5 5 21 43,97 -binding Ig-like lectin 14;Sialic acid-binding Ig-like lectin 5 MGAT3 Q09327 3 3 8,4 61,312 Beta-1,4-mannosyl-glycoprotein 4- beta-N-acetylglucosaminyltransferase MGAT5 Q09328 13 12 21,7 84,542 Alpha-1,6-mannosylglycoprotein 6- beta-N-acetylglucosaminyltransferase A AHNAK Q09666 24 24 15,1 629,09 Neuroblast differentiation-associated protein AHNAK FAM69C Q0P6D2;Q0P6D2-2 4 4 9,8 46,42 Protein FAM69C MGAT2 Q10469 11 11 30 51,55 Alpha-1,6-mannosyl-glycoprotein 2- beta-N-acetylglucosaminyltransferase GALNT2 Q10471;Q10471-2 21 20 43,6 64,732 Polypeptide N- acetylgalactosaminyltransferase 2;Polypeptide N- acetylgalactosaminyltransferase 2 soluble form GALNT1 Q10472 13 11 25,2 64,218 Polypeptide N- acetylgalactosaminyltransferase 1;Polypeptide N- acetylgalactosaminyltransferase 1 soluble form AP1B1 Q10567- 8 5 9,7 103,92 AP-1 complex subunit beta-1 2;Q10567;Q10567- 3;Q10567-4 BST1 Q10588-2;Q10588 4 4 21,5 29,326 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 BST2 Q10589-2;Q10589 2 2 8,9 18,394 Bone marrow stromal antigen 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ST3GAL1 Q11201 1 1 4,7 39,075 CMP-N-acetylneuraminate-beta- galactosamide-alpha-2,3- sialyltransferase 1 SCRN1 Q12765;Q12765- 4 4 13,5 46,382 Secernin-1 2;Q12765-3 HYAL1 Q12794- 5 5 23,7 45,144 -1 2;Q12794;Q12794- 7;Q12794-3;Q12794- 4;Q12794-6;Q12794-5

ASPH Q12797- 13 13 26,7 83,267 Aspartyl/asparaginyl beta-hydroxylase 10;Q12797;Q12797- 9;Q12797-6;Q12797- 5;Q12797-8;Q12797- 2;Q12797-7;Q12797- 4;Q12797-3

EFEMP1 Q12805-2;Q12805- 24 24 58,4 53,722 EGF-containing fibulin-like 4;Q12805- extracellular matrix protein 1 3;Q12805;Q12805-5

FSTL1 Q12841;Q12841-2 18 18 58,8 34,985 Follistatin-related protein 1 CNTN1 Q12860;Q12860-2 50 24 58,3 113,32 Contactin-1 CNTN1 Q12860-3 27 1 52 70,603 Contactin-1 MERTK Q12866 6 6 9,4 110,25 Tyrosine-protein kinase Mer TMEM115 Q12893 2 2 4,6 38,197 Transmembrane protein 115

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LMAN2 Q12907 13 13 46,6 40,228 Vesicular integral-membrane protein VIP36 PTPRJ Q12913-2;Q12913 7 7 16,5 57,189 Receptor-type tyrosine-protein phosphatase eta PDIA2 Q13087-2;Q13087 1 1 2,9 57,849 Protein disulfide-isomerase A2 MTAP Q13126-7;Q13126- 1 1 7,5 26,278 S-methyl-5-thioadenosine 4;Q13126;Q13126- phosphorylase 6;Q13126-5;Q13126- 3;Q13126-2

BAMBI Q13145 3 3 21,2 29,107 BMP and activin membrane-bound inhibitor homolog PSMD2 Q13200 1 1 2,8 100,2 26S proteasome non-ATPase regulatory subunit 2 MMRN1 Q13201-2;Q13201 4 4 9,4 58,169 Multimerin-1;Platelet glycoprotein Ia*;155 kDa platelet multimerin SEMA3B Q13214-2;Q13214 14 14 28,7 83,034 Semaphorin-3B DNAJC3 Q13217 17 17 43,3 57,579 DnaJ homolog subfamily C member 3 SELENBP1 Q13228;Q13228- 23 23 60 52,39 Selenium-binding protein 1 4;Q13228-2;Q13228-3

CHIT1 Q13231- 13 13 49,4 48,564 Chitotriosidase-1 3;Q13231;Q13231- 4;Q13231-2 NME3 Q13232 2 2 15,4 19,015 Nucleoside diphosphate kinase 3 NOG Q13253 1 1 5,2 25,774 Noggin GRM1 Q13255;Q13255- 3 3 3,2 132,36 Metabotropic glutamate receptor 1 2;Q13255-3 SEMA3F Q13275-2;Q13275 8 8 14,7 85,063 Semaphorin-3F

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PTK7 Q13308-4;Q13308- 5 5 7,4 112,26 Inactive tyrosine-protein kinase 7 5;Q13308;Q13308- 6;Q13308-3;Q13308-2

DYNC1I2 Q13409-6;Q13409- 1 1 2,5 68,297 Cytoplasmic dynein 1 intermediate 3;Q13409-7;Q13409- chain 2 2;Q13409-5;Q13409

MSLN Q13421-4;Q13421- 10 10 22,2 67,94 Mesothelin;- 3;Q13421-2;Q13421 potentiating factor;Mesothelin, cleaved form NNT Q13423 1 1 1,8 113,89 NAD(P) transhydrogenase, mitochondrial ADAM9 Q13443-2;Q13443 6 6 10,5 72,359 Disintegrin and metalloproteinase domain-containing protein 9 ADAM15 Q13444-10;Q13444- 6 6 9,5 83,664 Disintegrin and metalloproteinase 9;Q13444-8;Q13444- domain-containing protein 15 2;Q13444-7;Q13444- 6;Q13444-12;Q13444- 5;Q13444-4;Q13444- 3;Q13444;Q13444- 11;Q13444-13

LSAMP Q13449 11 11 37,9 37,393 Limbic system-associated membrane protein SQSTM1 Q13501-2;Q13501 4 4 21,9 38,629 Sequestosome-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ART3 Q13508;Q13508- 12 12 32,6 43,923 Ecto-ADP-ribosyltransferase 3 2;Q13508-3 ASAH1 Q13510;Q13510- 8 8 24,1 44,659 Acid ceramidase;Acid ceramidase 2;Q13510-3 subunit alpha;Acid ceramidase subunit beta PNOC Q13519;Q13519-2 3 3 30,7 20,295 Prepronociceptin;Neuropeptide 1;;Neuropeptide 2 CAMK2B Q13554-4;Q13554- 6 5 20,3 54,073 Calcium/calmodulin-dependent 8;Q13554-5;Q13554- protein kinase type II subunit beta 2;Q13554;Q13554- 7;Q13554-3;Q13554-6

CAMK2G Q13555-10;Q13555- 2 2 6,9 55,96 Calcium/calmodulin-dependent 3;Q13555-5;Q13555- protein kinase type II subunit gamma 4;Q13555-7;Q13555- 9;Q13555-2;Q13555- 8;Q13555;Q13555-6

CAMK2D Q13557-8;Q13557- 5 4 15,9 54,127 Calcium/calmodulin-dependent 12;Q13557-9;Q13557- protein kinase type II subunit delta 10;Q13557- 5;Q13557;Q13557- 3;Q13557-6;Q13557- 4;Q13557-11

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CDH18 Q13634-2;Q13634 4 4 11,3 63,676 Cadherin-18 TPBG Q13641 3 3 8,3 46,031 Trophoblast glycoprotein ALCAM Q13740- 23 23 47,2 63,664 CD166 antigen 2;Q13740;Q13740- 3;Q13740-4 APOF Q13790 3 3 11,7 35,399 Apolipoprotein F ENPP2 Q13822;Q13822- 46 46 67 98,993 Ectonucleotide 3;Q13822-2;O14638 /phosphodiesterase family member 2 BLMH Q13867 7 7 21,1 52,562 Bleomycin hydrolase BMPR2 Q13873;Q13873-2 3 3 3,2 115,2 Bone morphogenetic protein receptor type-2 COTL1 Q14019 5 5 39,4 15,945 Coactosin-like protein COL9A2 Q14055 2 2 3,2 65,13 Collagen alpha-2(IX) chain COX17 Q14061 1 1 20,6 6,9151 Cytochrome c oxidase copper chaperone HNRNPD Q14103-4;Q14103- 1 1 4,9 30,672 Heterogeneous nuclear 3;Q14103-2;Q14103 ribonucleoprotein D0

NID2 Q14112;Q14112-2 32 31 35,1 151,25 Nidogen-2 LRP8 Q14114- 9 9 14,9 99,091 Low-density lipoprotein receptor- 3;Q14114;Q14114- related protein 8 2;Q14114-4 DAG1 Q14118 18 18 28,9 97,44 ;Alpha-dystroglycan;Beta- dystroglycan DSG2 Q14126 12 12 15,7 122,29 -2 MLEC Q14165 9 9 37,3 32,233 Malectin Q14195-2 1 1 2,8 73,91

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DCTN1 Q14203-5;Q14203- 1 1 1,1 126,73 subunit 1 2;Q14203-3;Q14203- 4;Q14203-6;Q14203

EBI3 Q14213 2 2 9,6 25,396 Interleukin-27 subunit beta RCN2 Q14257;Q14257-2 9 9 32,5 36,876 Reticulocalbin-2 FGL2 Q14314 4 4 13,2 50,228 Fibroleukin GAS6 Q14393-2;Q14393- 19 19 38,6 74,925 Growth arrest-specific protein 6 3;Q14393;Q14393- 5;Q14393-4 PDE3A Q14432 2 2 3,3 124,98 cGMP-inhibited 3,5-cyclic phosphodiesterase A WFDC2 Q14508;Q14508- 6 6 67,7 12,993 WAP four-disulfide core domain 2;Q14508-3;Q14508- protein 2 4;Q14508-5

SPARCL1 Q14515;Q14515-2 34 34 66,3 75,207 SPARC-like protein 1 FAT1 Q14517 18 18 5,3 506,27 Protocadherin Fat 1;Protocadherin Fat 1, nuclear form HABP2 Q14520-2;Q14520 18 18 37,5 59,864 Hyaluronan-binding protein 2;Hyaluronan-binding protein 2 50 kDa heavy chain;Hyaluronan-binding protein 2 50 kDa heavy chain alternate form;Hyaluronan-binding protein 2 27 kDa light chain;Hyaluronan-binding protein 2 27 kDa light chain alternate form SEMA3A Q14563 4 4 7 88,888 Semaphorin-3A DSC3 Q14574-2;Q14574 4 4 4,2 93,453 Desmocollin-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] NBR1 Q14596-2;Q14596 3 3 5,8 103,83 Next to BRCA1 gene 1 protein ITIH4 Q14624;Q14624- 39 3 48,6 103,36 Inter-alpha-trypsin inhibitor heavy 3;Q14624- chain H4;70 kDa inter-alpha-trypsin 4;CON__Q3T052 inhibitor heavy chain H4;35 kDa inter- alpha-trypsin inhibitor heavy chain H4 ITIH4 Q14624-2 37 1 49 101,24 Inter-alpha-trypsin inhibitor heavy chain H4;70 kDa inter-alpha-trypsin inhibitor heavy chain H4;35 kDa inter- alpha-trypsin inhibitor heavy chain H4 MESDC2 Q14696 4 4 23,5 26,076 LDLR chaperone MESD GANAB Q14697;Q14697-2 17 17 22 106,87 Neutral alpha-glucosidase AB LTBP1 Q14766;Q14766- 27 26 21,3 186,79 Latent-transforming growth factor 4;Q14766-2;Q14766- beta-binding protein 1 5;Q14766-3

LTBP2 Q14767 22 22 21 195,05 Latent-transforming growth factor beta-binding protein 2 GRM3 Q14832-2;Q14832 1 1 3 60,749 Metabotropic glutamate receptor 3 LASP1 Q14847;Q14847- 4 4 19,9 29,717 LIM and SH3 domain protein 1 2;Q14847-3;O76041-2

CRYM Q14894 6 6 28,7 33,775 Ketimine reductase mu-crystallin GPNMB Q14956-2;Q14956 2 2 4,8 62,642 Transmembrane glycoprotein NMB OPCML Q14982-3;Q14982- 9 8 31,2 33,574 -binding protein/cell adhesion 2;Q14982;Q14982-4 molecule

TMEM132D Q14C87;Q14C87-2 20 20 23,1 122,31 Transmembrane protein 132D HEPACAM Q14CZ8;Q14CZ8-2 4 4 14,9 46,026 Hepatocyte cell adhesion molecule TMEM132B Q14DG7;Q14DG7- 9 9 12,7 119,48 Transmembrane protein 132B 3;Q14DG7-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SLC39A14 Q15043-2;Q15043- 3 3 9,4 52,838 Zinc transporter ZIP14 3;Q15043 PDIA6 Q15084- 6 6 24 47,837 Protein disulfide-isomerase A6 3;Q15084;Q15084- 4;Q15084-5;Q15084-2

PCOLCE Q15113 20 20 60,4 47,972 Procollagen C-endopeptidase enhancer 1 PEA15 Q15121;Q15121-2 3 3 36,9 15,04 Astrocytic phosphoprotein PEA-15 PCM1 Q15154-2;Q15154 3 3 2,7 222,22 Pericentriolar material 1 protein PON2 Q15165-3;Q15165- 4 4 14,9 37,996 Serum paraoxonase/arylesterase 2 1;Q15165 PON3 Q15166 4 4 14,1 39,607 Serum paraoxonase/lactonase 3 PDGFRL Q15198 2 2 8,3 41,86 Platelet-derived growth factor receptor-like protein PVRL1 Q15223;Q15223- 7 7 23,4 57,157 -1 3;Q15223-2 PTPRR Q15256;Q15256-5 5 5 9 73,833 Receptor-type tyrosine-protein phosphatase R PTPRK Q15262;Q15262- 8 8 7,3 162,1 Receptor-type tyrosine-protein 2;Q15262-3;Q15262-4 phosphatase kappa

RCN1 Q15293;Q15293-2 7 7 22,4 38,89 Reticulocalbin-1 ERBB4 Q15303-4;Q15303- 7 7 5,5 143,97 Receptor tyrosine-protein kinase erbB- 3;Q15303-2;Q15303 4;ERBB4 intracellular domain

PCBP1 Q15365 1 1 3,9 37,497 Poly(rC)-binding protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] EPHA7 Q15375- 7 5 10,3 111,62 Ephrin type-A receptor 7 4;Q15375;Q15375- 3;Q15375-5;Q15375-2

PPP1R7 Q15435- 3 3 12 36,837 regulatory 2;Q15435;Q15435- subunit 7 5;Q15435-4;Q15435-3

SF3A1 Q15459-2;Q15459 1 1 1,8 81,677 Splicing factor 3A subunit 1 SHH Q15465 2 2 3,7 49,607 protein;Sonic hedgehog protein N-product;Sonic hedgehog protein C-product FCN2 Q15485-2;Q15485 1 1 5,1 30,227 Ficolin-2 RGN Q15493;Q15493-2 4 4 21,7 33,252 CDSN Q15517 1 1 3,4 51,522 MAPRE2 Q15555-4;Q15555- 2 2 9,9 30,691 Microtubule-associated protein RP/EB 5;Q15555-3;Q15555 family member 2

TGFBI Q15582 27 27 48,2 74,68 Transforming growth factor-beta- induced protein ig-h3 TSN Q15631 1 1 6,6 26,183 Translin MAPRE1 Q15691 2 2 10,4 29,999 Microtubule-associated protein RP/EB family member 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MYLK Q15746-11;Q15746- 2 2 3,1 110,07 kinase, smooth 7;Q15746-4;Q15746- muscle;Myosin light chain kinase, 5;Q15746-2;Q15746- smooth muscle, deglutamylated form 3;Q15746- 6;Q15746;Q15746- 10;Q15746-8;Q15746-9

EFNB3 Q15768 7 7 24,7 35,834 Ephrin-B3 CHI3L2 Q15782- 9 9 33,4 42,508 Chitinase-3-like protein 2 6;Q15782;Q15782-5

NPTX1 Q15818 14 14 37,7 47,122 Neuronal pentraxin-1 UBE2V2 Q15819 4 1 31,7 16,363 Ubiquitin-conjugating enzyme E2 variant 2 CST6 Q15828 6 6 62,4 16,511 Cystatin-M NEDD8 Q15843 3 3 23,5 9,0714 NEDD8 CLUL1 Q15846 6 6 21 54,214 Clusterin-like protein 1 ADIRF Q15847 2 2 59,2 7,8547 Adipogenesis regulatory factor ATP6AP1 Q15904 7 7 18,5 52,025 V-type proton ATPase subunit S1 SNCB Q16143 2 2 28,4 14,288 Beta-synuclein IGFBP7 Q16270-2;Q16270 11 11 45,9 28,86 Insulin-like growth factor-binding protein 7 NTRK3 Q16288-2;Q16288- 5 5 11,4 68,452 NT-3 growth factor receptor 5;Q16288-3;Q16288- 4;Q16288

LAMA4 Q16363-2;Q16363 18 18 13,1 201,77 Laminin subunit alpha-4 EXT1 Q16394;Q92935 3 3 4,4 86,254 Exostosin-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DDB1 Q16531 8 8 7,9 126,97 DNA damage-binding protein 1 CDC37 Q16543 1 1 4,5 44,468 Hsp90 co-chaperone Cdc37;Hsp90 co- chaperone Cdc37, N-terminally processed DPYSL2 Q16555- 6 6 17 58,162 Dihydropyrimidinase-related protein 2 2;Q16555;Q14194;Q14 194-2 CAMK4 Q16566 1 1 3 51,925 Calcium/calmodulin-dependent protein kinase type IV CARTPT Q16568 6 6 45,7 12,829 Cocaine- and -regulated transcript protein;CART(1- 39);CART(42-89) C3AR1 Q16581 1 1 5,6 53,864 C3a anaphylatoxin chemotactic receptor ECM1 Q16610;Q16610- 24 24 60,2 60,673 Extracellular matrix protein 1 4;Q16610-2;Q16610-3

NTRK2 Q16620-2;Q16620- 6 6 20,5 53,051 BDNF/NT-3 growth factors receptor 3;Q16620-5;Q16620- 6;Q16620;Q16620- 4;Q16620-7

STX1A Q16623-3;Q16623- 1 1 5,6 28,994 Syntaxin-1A 2;Q16623 CCL14 Q16627;Q16627-2 4 4 47,3 10,678 C-C motif chemokine 14;HCC-1(3- 74);HCC-1(4-74);HCC-1(9-74) PRSS8 Q16651-2;Q16651 1 1 11,4 30,519 Prostasin;Prostasin light chain;Prostasin heavy chain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MOG Q16653-10;Q16653- 4 4 28,7 19,334 Myelin-oligodendrocyte glycoprotein 9;Q16653-8;Q16653- 11;Q16653-2;Q16653- 6;Q16653-3;Q16653- 7;Q16653;Q16653- 5;Q16653-13

FSCN1 Q16658 9 9 29,2 54,529 Fascin MIA Q16674 4 4 48,1 14,509 -derived growth regulatory protein MAN2A1 Q16706 30 29 29,9 131,14 Alpha-mannosidase 2 QPCT Q16769;Q16769-2 7 7 32,1 40,876 Glutaminyl-peptide cyclotransferase HAGH Q16775- 4 4 16,9 28,86 Hydroxyacylglutathione hydrolase, 2;Q16775;Q16775-3 mitochondrial

RTN1 Q16799 5 5 11,6 83,617 Reticulon-1 PTPRO Q16827-5;Q16827- 1 1 2,3 67,671 Receptor-type tyrosine-protein 2;Q16827 phosphatase O DDR2 Q16832 1 1 1,8 96,735 Discoidin domain-containing receptor 2 PTPRN Q16849;Q16849- 11 11 15 105,85 Receptor-type tyrosine-protein 3;Q16849-2 phosphatase-like N AOC3 Q16853- 2 2 5,8 70,674 Membrane primary amine oxidase 2;Q16853;Q16853-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TXNRD1 Q16881-7;Q16881- 2 2 7,8 50,873 Thioredoxin reductase 1, cytoplasmic 5;Q16881-2;Q16881- 4;Q16881-3;Q16881- 6;Q16881

MSMP Q1L6U9 1 1 9,4 14,993 Prostate-associated microseminoprotein TMEM132A Q24JP5;Q24JP5- 22 22 28 110,11 Transmembrane protein 132A 2;Q24JP5-4;Q24JP5-3

VWC2 Q2TAL6 7 7 35,4 35,282 Brorin COL28A1 Q2UY09;Q2UY09- 7 7 7,8 116,66 Collagen alpha-1(XXVIII) chain 3;Q2UY09-2 GNPTAB Q3T906 2 2 2,7 143,62 N-acetylglucosamine-1- phosphotransferase subunits alpha/beta;N-acetylglucosamine-1- phosphotransferase subunit alpha;N- acetylglucosamine-1- phosphotransferase subunit beta FUT11 Q495W5;Q495W5-2 5 5 15 55,815 Alpha-(1,3)-fucosyltransferase 11

NRN1L Q496H8 1 1 8,5 17,786 Neuritin-like protein SV2C Q496J9 1 1 2,1 82,341 glycoprotein 2C CCSMST1 Q4G0I0 3 3 25 15,004 Protein CCSMST1 GXYLT1 Q4G148-2;Q4G148 2 2 4,9 46,8 Glucoside 1 SVEP1 Q4LDE5;Q4LDE5- 7 7 3,3 390,17 Sushi, von Willebrand factor type A, 4;Q4LDE5-2;Q4LDE5-3 EGF and pentraxin domain-containing protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] FNDC1 Q4ZHG4-2;Q4ZHG4 1 1 1,3 198,69 Fibronectin type III domain-containing protein 1 SLC39A12 Q504Y0-5;Q504Y0- 3 3 7 61,642 Zinc transporter ZIP12 3;Q504Y0- 4;Q504Y0;Q504Y0-2

PKDCC Q504Y2 3 3 9,9 54,131 Protein kinase domain-containing protein, cytoplasmic SEZ6 Q53EL9- 17 17 25,2 107,45 Seizure protein 6 homolog 3;Q53EL9;Q53EL9- 2;Q53EL9-4 PDLIM3 Q53GG5-3;Q53GG5- 1 1 7,9 20,214 PDZ and LIM domain protein 3 2;Q53GG5 PLA1A Q53H76-4;Q53H76- 3 3 15,9 31,285 member A 3;Q53H76;Q53H76-2

FBLN7 Q53RD9;Q53RD9- 9 9 23,9 47,375 Fibulin-7 4;Q53RD9-2;Q53RD9-3

ASPRV1 Q53RT3 1 1 4,1 36,991 Retroviral-like 1 SPRN Q5BIV9 1 1 16,6 14,522 Shadow of prion protein C4orf48 Q5BLP8- 5 5 40,3 14,747 Neuropeptide-like protein C4orf48 2;Q5BLP8;Q5BLP8-3

PRRT3 Q5FWE3-3;Q5FWE3 6 6 20 44,108 Proline-rich transmembrane protein 3

FREM1 Q5H8C1;Q5H8C1-2 3 3 1,9 244,15 FRAS1-related extracellular matrix protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MIA3 Q5JRA6- 16 16 9,8 206,89 Melanoma inhibitory activity protein 3 2;Q5JRA6;Q5JRA6-3

NHLRC3 Q5JS37-2;Q5JS37 3 3 13,9 31,054 NHL repeat-containing protein 3 EPHA10 Q5JZY3-3;Q5JZY3 6 1 8,5 97,292 Ephrin type-A receptor 10 EPHA10 Q5JZY3-2 6 1 25,8 32,12 Ephrin type-A receptor 10 COLEC12 Q5KU26 8 8 8,4 81,514 Collectin-12 ELFN2 Q5R3F8 2 2 3 89,686 Protein phosphatase 1 regulatory subunit 29 PPM1L Q5SGD2-2;Q5SGD2- 2 2 16,6 20,324 Protein phosphatase 1L 3;Q5SGD2 FREM2 Q5SZK8-2;Q5SZK8 9 9 4,9 295,84 FRAS1-related extracellular matrix protein 2 HYI Q5T013-3;Q5T013 1 1 5,3 26,873 Putative hydroxypyruvate isomerase FAM83B Q5T0W9 1 1 0,9 114,8 Protein FAM83B CHCHD2;CHCHD2P9 Q9Y6H1;Q5T1J5 1 1 8,6 15,512 Coiled-coil-helix-coiled-coil-helix domain-containing protein 2, mitochondrial;Putative coiled-coil- helix-coiled-coil-helix domain- containing protein CHCHD2P9, mitochondrial GPR158 Q5T848 2 2 2,6 135,49 Probable G-protein coupled receptor 158 WLS Q5T9L3;Q5T9L3-2 1 1 1,8 62,253 Protein wntless homolog DDI2 Q5TDH0- 3 3 27 23,72 Protein DDI1 homolog 2 2;Q5TDH0;Q5TDH0-3

MANEAL Q5VSG8;Q5VSG8- 6 6 18,6 51,316 Glycoprotein endo-alpha-1,2- 3;Q5VSG8-2 mannosidase-like protein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CACHD1 Q5VU97;Q5VU97-2 16 16 15,9 142,29 VWFA and cache domain-containing protein 1 FAM171A1 Q5VUB5 1 1 1,2 97,853 Protein FAM171A1 KIAA0319 Q5VV43-4;Q5VV43- 7 7 6,7 110,37 Dyslexia-associated protein KIAA0319 2;Q5VV43;Q5VV43-3

ATRNL1 Q5VV63-2;Q5VV63 2 2 7,1 51,867 Attractin-like protein 1 C1QL3 Q5VWW1;Q5VWW1- 6 4 40,4 26,719 Complement C1q-like protein 3 3;Q5VWW1-2 PEAR1 Q5VY43 1 1 2 110,67 Platelet endothelial aggregation receptor 1 CD276 Q5ZPR3-3;Q5ZPR3- 3 3 12,6 52,761 CD276 antigen 4;Q5ZPR3;Q5ZPR3-2

EGFLAM Q63HQ2- 13 13 15 110,34 Pikachurin 2;Q63HQ2;Q63HQ2- 4;Q63HQ2-3 METRNL Q641Q3-2;Q641Q3 5 5 41,5 25,738 Meteorin-like protein WSCD1 Q658N2 4 4 9,9 65,693 WSC domain-containing protein 1 CPZ Q66K79;Q66K79- 4 4 10,6 73,655 Carboxypeptidase Z 2;Q66K79-3 OLFML2A Q68BL7- 3 3 10 68,89 Olfactomedin-like protein 2A 2;Q68BL7;Q68BL7-3

OLFML2B Q68BL8;Q68BL8-2 6 6 10,1 83,998 Olfactomedin-like protein 2B NCR3LG1 Q68D85 4 4 11 50,827 Natural cytotoxicity triggering receptor 3 ligand 1 POLR2M Q6EEV4-2;Q6EEV4 1 1 27,9 8,8268 DNA-directed RNA polymerase II subunit GRINL1A, isoforms 4/5 VASN Q6EMK4 5 5 10 71,712 Vasorin

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SFRP4 Q6FHJ7 7 7 24,9 39,826 Secreted -related protein 4 LAIR1 Q6GTX8-4;Q6GTX8- 2 2 12,4 23,049 Leukocyte-associated immunoglobulin- 3;Q6GTX8-2;Q6GTX8 like receptor 1

TWF2 Q6IBS0 2 2 8,3 39,548 Twinfilin-2 TMEM132E Q6IEE7 12 12 17,7 107,09 Transmembrane protein 132E WBSCR17 Q6IS24 4 4 8 67,75 Putative polypeptide N- acetylgalactosaminyltransferase-like protein 3 FSTL4 Q6MZW2;Q6MZW2- 25 23 37,8 93,095 Follistatin-related protein 4 3;Q6MZW2-2 TCTN3 Q6NUS6- 2 2 6,3 47,984 Tectonic-3 2;Q6NUS6;Q6NUS6- 4;Q6NUS6-3;Q6NUS6-5

RGMB Q6NW40 8 8 34,3 47,546 RGM domain family member B ERAP2 Q6P179- 6 6 6,1 105,52 Endoplasmic reticulum 3;Q6P179;Q6P179- aminopeptidase 2 2;Q6P179-4 CASC4 Q6P4E1- 11 11 24,6 47,308 Protein CASC4 5;Q6P4E1;Q6P4E1- 4;Q6P4E1-2;Q6P4E1-3

FAHD1 Q6P587;Q6P587- 2 2 13,4 24,843 Acylpyruvase FAHD1, mitochondrial 2;Q6P587-3 GALNT18 Q6P9A2;Q6P9A2-2 9 9 17,8 69,56 Polypeptide N- acetylgalactosaminyltransferase 18 VWA1 Q6PCB0 5 5 19,1 46,804 von Willebrand factor A domain- containing protein 1 CPLX2 Q6PUV4 2 2 28,4 15,394 Complexin-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CSPG4 Q6UVK1 30 30 19,4 250,53 Chondroitin sulfate MOXD1 Q6UVY6-2;Q6UVY6 1 1 1,8 62,7 DBH-like monooxygenase protein 1 CBLN3 Q6UW01 7 7 36,6 21,52 Cerebellin-3 SPESP1 Q6UW49 1 1 8,3 38,931 Sperm equatorial segment protein 1 FAM198B Q6UWH4;Q6UWH4- 9 9 21,8 57,552 Protein FAM198B 2;Q6UWH4-3 SBSN Q6UWP8-2;Q6UWP8 3 3 17 25,335 Suprabasin

ENPP6 Q6UWR7 9 9 26,4 50,24 Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 OLFML1 Q6UWY5 4 4 14,9 45,95 Olfactomedin-like protein 1 LAYN Q6UX15-2;Q6UX15 2 2 4,3 42,28 Layilin PLXDC2 Q6UX71;Q6UX71-2 14 14 25,9 59,582 Plexin domain-containing protein 2 B3GNT9 Q6UX72 2 2 8 43,751 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 9 C16orf89 Q6UX73-2;Q6UX73 11 11 47,1 40,612 UPF0764 protein C16orf89 PI16 Q6UXB8;Q6UXB8-2 9 9 27,4 49,471 Peptidase inhibitor 16 SEZ6L2 Q6UXD5-3;Q6UXD5- 14 13 26,4 92,454 Seizure 6-like protein 2 5;Q6UXD5-6;Q6UXD5- 2;Q6UXD5;Q6UXD5-4

CRELD2 Q6UXH1-3;Q6UXH1- 2 2 9,9 30,712 Cysteine-rich with EGF-like domain 2;Q6UXH1- protein 2 4;Q6UXH1;Q6UXH1- 6;Q6UXH1-5 PAMR1 Q6UXH9-2;Q6UXH9- 8 8 13 81,942 Inactive serine protease PAMR1 3;Q6UXH9

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] VIT Q6UXI7-2;Q6UXI7- 4 4 6,4 71,706 Vitrin 5;Q6UXI7;Q6UXI7- 4;Q6UXI7-3 NPNT Q6UXI9- 3 3 6,3 58,651 Nephronectin 5;Q6UXI9;Q6UXI9- 4;Q6UXI9-6;Q6UXI9- 3;Q6UXI9-2

ISLR2 Q6UXK2 6 6 13,8 78,989 Immunoglobulin superfamily containing leucine-rich repeat protein 2 LRRN1 Q6UXK5 10 10 14,7 80,716 Leucine-rich repeat neuronal protein 1 DLK2 Q6UY11-2;Q6UY11 2 2 13,2 21,33 Protein delta homolog 2 NAPRT Q6XQN6- 2 2 9,9 56,099 Nicotinate phosphoribosyltransferase 3;Q6XQN6;Q6XQN6-2

CD109 Q6YHK3;Q6YHK3- 24 24 23,9 161,69 CD109 antigen 4;Q6YHK3-2;Q6YHK3-3

GLDN Q6ZMI3-2;Q6ZMI3 2 2 4,9 45,822 Gliomedin ADAMTSL5 Q6ZMM2-2;Q6ZMM2 2 2 7,1 53,17 ADAMTS-like protein 5

THSD4 Q6ZMP0;Q6ZMP0- 6 6 9,2 112,45 Thrombospondin type-1 domain- 4;Q6ZMP0-2;Q6ZMP0- containing protein 4 3 UNC5A Q6ZN44-2;Q6ZN44 1 1 3,3 33,342 Netrin receptor UNC5A ARHGAP36 Q6ZRI8-3;Q6ZRI8- 3 3 16,1 46,229 Rho GTPase-activating protein 36 5;Q6ZRI8-2;Q6ZRI8- 4;Q6ZRI8 QSOX2 Q6ZRP7 14 14 27,9 77,528 Sulfhydryl oxidase 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] KIAA1549L Q6ZVL6 10 1 6,5 199 UPF0606 protein KIAA1549L KIAA1549L Q6ZVL6-2 10 1 10,2 131,2 UPF0606 protein KIAA1549L TOM1L2 Q6ZVM7-2;Q6ZVM7- 2 2 7,4 49,963 TOM1-like protein 2 3;Q6ZVM7- 5;Q6ZVM7;Q6ZVM7-4

CHSY3 Q70JA7 1 1 2,2 100,28 Chondroitin sulfate synthase 3 ILDR2 Q71H61 1 1 2,2 71,199 Immunoglobulin-like domain- containing receptor 2 B4GALNT4 Q76KP1 9 9 10,6 116,51 N-acetyl-beta-glucosaminyl- glycoprotein 4-beta-N- acetylgalactosaminyltransferase 1 ADAMTS13 Q76LX8-3;Q76LX8- 1 1 1 144,52 A disintegrin and metalloproteinase 2;Q76LX8 with thrombospondin motifs 13 CCDC80 Q76M96;Q76M96-2 1 1 1,4 108,17 Coiled-coil domain-containing protein 80 BTN2A2;BTN2A1 Q8WVV5-3;Q7KYR7- 1 1 4,3 28,927 Butyrophilin subfamily 2 member 6;Q7KYR7-4;Q8WVV5- A2;Butyrophilin subfamily 2 member 2;Q7KYR7- A1 5;Q8WVV5;Q7KYR7;Q7 KYR7-1

TRIL Q7L0X0 1 1 1,4 88,722 TLR4 interactor with leucine rich repeats SV2B Q7L1I2 1 1 2,3 77,444 Synaptic vesicle glycoprotein 2B ASRGL1 Q7L266-2;Q7L266 2 2 16,1 18,98 Isoaspartyl peptidase/L- asparaginase;Isoaspartyl peptidase/L- asparaginase alpha chain;Isoaspartyl peptidase/L-asparaginase beta chain

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SYT13 Q7L8C5 1 1 3,5 46,884 Synaptotagmin-13 LINGO2 Q7L985 4 3 7,9 68,065 Leucine-rich repeat and immunoglobulin-like domain- containing nogo receptor-interacting protein 2 CHST15 Q7LFX5;Q7LFX5-2 10 10 19,6 64,925 Carbohydrate sulfotransferase 15 CHST3 Q7LGC8 3 3 10 54,705 Carbohydrate sulfotransferase 3 MAMDC2 Q7Z304 2 2 4,1 77,555 MAM domain-containing protein 2 NEGR1 Q7Z3B1;Q7Z3B1-2 11 11 38,1 38,719 Neuronal growth regulator 1 NOTCH2NL Q7Z3S9;Q7Z3S9-3 3 1 22,5 25,835 Notch homolog 2 N-terminal-like protein GDF7 Q7Z4P5 1 1 4 46,95 Growth/differentiation factor 7 C6orf120 Q7Z4R8 2 2 34 20,772 UPF0669 protein C6orf120 MDGA2 Q7Z553;Q7Z553- 14 14 23,8 107,43 MAM domain-containing 3;Q7Z553-2 glycosylphosphatidylinositol anchor protein 2 FAM19A5 Q7Z5A7-2;Q7Z5A7- 3 3 33,6 13,592 Protein FAM19A5 3;Q7Z5A7 FAM19A3 Q7Z5A8 1 1 10,5 14,776 Protein FAM19A3 FAM19A1 Q7Z5A9 3 3 33,1 14,901 Protein FAM19A1 VMO1 Q7Z5L0 1 1 8,4 21,534 Vitelline membrane outer layer protein 1 homolog PODN Q7Z5L7- 9 9 27 57,895 Podocan 4;Q7Z5L7;Q7Z5L7- 2;Q7Z5L7-3 SDK1 Q7Z5N4-3;Q7Z5N4 3 3 2,1 240,02 Protein sidekick-1 PRRT2 Q7Z6L0- 5 5 38,5 30,652 Proline-rich transmembrane protein 2 3;Q7Z6L0;Q7Z6L0-2 MILR1 Q7Z6M3-2;Q7Z6M3 1 1 4,8 27,959 Allergin-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ABI3BP Q7Z7G0;Q7Z7G0- 11 11 14,1 118,64 Target of Nesh-SH3 2;Q7Z7G0-3;Q7Z7G0-4

TMED4 Q7Z7H5-3;Q7Z7H5- 7 6 41,4 20,781 Transmembrane emp24 domain- 2;Q7Z7H5 containing protein 4 MEGF8 Q7Z7M0;Q7Z7M0-2 44 44 27,7 303,1 Multiple epidermal growth factor-like domains protein 8 B3GNT8 Q7Z7M8 2 2 5,8 43,395 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 8 GALNT5 Q7Z7M9 1 1 1,2 106,26 Polypeptide N- acetylgalactosaminyltransferase 5 GALNT7 Q86SF2 15 15 34,6 75,388 N-acetylgalactosaminyltransferase 7 GPR126 Q86SQ4- 2 2 2,5 133,67 G-protein coupled receptor 126 2;Q86SQ4;Q86SQ4- 4;Q86SQ4-3 GALNT10 Q86SR1;Q86SR1- 12 12 25,7 68,991 Polypeptide N- 2;Q86SR1-3;Q86SR1- acetylgalactosaminyltransferase 10 4;Q49A17-2;Q49A17

CLEC14A Q86T13 1 1 3,3 51,635 C-type lectin domain family 14 member A ADAMTSL2 Q86TH1 7 7 14,4 104,62 ADAMTS-like protein 2 C14orf37 Q86TY3-2;Q86TY3 4 4 4,8 72,067 Uncharacterized protein C14orf37 OAF Q86UD1 9 9 40,3 30,688 Out at first protein homolog RTN4RL1 Q86UN2 4 4 14,7 49,065 Reticulon-4 receptor-like 1 RTN4RL2 Q86UN3;Q86UN3-2 7 7 21,4 46,105 Reticulon-4 receptor-like 2

HAPLN4 Q86UW8 3 3 12,2 42,801 Hyaluronan and proteoglycan link protein 4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ITIH5 Q86UX2;Q86UX2- 27 27 34,1 104,58 Inter-alpha-trypsin inhibitor heavy 3;Q86UX2-2;Q86UX2-4 chain H5

GPR180 Q86V85 2 2 5,7 49,395 Integral membrane protein GPR180 CD163 Q86VB7-3;Q86VB7- 22 22 30,5 121,61 Scavenger receptor cysteine-rich type 4;Q86VB7;Q86VB7-2 1 protein M130;Soluble CD163

CAND1 Q86VP6-2;Q86VP6 3 3 3,9 117,89 Cullin-associated NEDD8-dissociated protein 1 LRP11 Q86VZ4;Q86VZ4-2 8 8 24,8 53,311 Low-density lipoprotein receptor- related protein 11 AMIGO1 Q86WK6 2 2 5,3 55,239 Amphoterin-induced protein 1 LSR Q86X29-6;Q86X29- 6 6 24,7 54,498 Lipolysis-stimulated lipoprotein 5;Q86X29-3;Q86X29- receptor 4;Q86X29;Q86X29-2

TMED7 Q86XR7-2;Q9Y3B3- 6 6 16,1 46,172 Transmembrane emp24 domain- 2;Q9Y3B3 containing protein 7 FRAS1 Q86XX4;Q86XX4- 4 4 2 443,21 Extracellular matrix protein FRAS1 2;Q86XX4-5;Q86XX4- 4;Q86XX4-6

COL23A1 Q86Y22 2 2 5,4 51,943 Collagen alpha-1(XXIII) chain XYLT1 Q86Y38 14 14 16,4 107,57 Xylosyltransferase 1 STX12 Q86Y82 4 4 22,1 31,642 Syntaxin-12 TMEM25 Q86YD3-5;Q86YD3- 2 2 9,5 33,011 Transmembrane protein 25 2;Q86YD3- 4;Q86YD3;Q86YD3-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LDLRAD3 Q86YD5 1 1 4,9 37,418 Low-density lipoprotein receptor class A domain-containing protein 3 AMICA1 Q86YT9-3;Q86YT9- 2 2 8,1 29,422 Junctional adhesion molecule-like 4;Q86YT9-2;Q86YT9

GALNT13 Q8IUC8;Q8IUC8- 10 8 22,3 64,05 Polypeptide N- 3;Q8IUC8-2 acetylgalactosaminyltransferase 13 PLXDC1 Q8IUK5;Q8IUK5- 7 7 20,6 55,76 Plexin domain-containing protein 1 3;Q8IUK5-2;Q8IUK5-4

CBLN2 Q8IUK8 5 3 30,8 24,084 Cerebellin-2 AEBP1 Q8IUX7;Q8IUX7-2 20 19 21,1 130,93 Adipocyte enhancer-binding protein 1 PLD3 Q8IV08 9 9 23,7 54,705 Phospholipase D3 GPIHBP1 Q8IV16 1 1 14,1 19,806 Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 PCP2 Q8IVA1-2;Q8IVA1 3 3 40 12,825 Purkinje cell protein 2 homolog SBSPON Q8IVN8 2 2 11,7 29,61 Somatomedin-B and thrombospondin type-1 domain-containing protein CARKD Q8IW45;Q8IW45- 3 3 9,5 36,576 ATP-dependent (S)-NAD(P)H-hydrate 2;Q8IW45-4;Q8IW45-3 dehydratase

SLITRK4 Q8IW52 8 8 13,7 94,33 SLIT and NTRK-like protein 4 GPR125 Q8IWK6-4;Q8IWK6- 1 1 3,7 42,972 Probable G-protein coupled receptor 2;Q8IWK6-3;Q8IWK6 125

BRSK2 Q8IWQ3-4 1 1 1,9 77,597 Serine/threonine-protein kinase BRSK2 SCN4B Q8IWT1;Q8IWT1-2 3 3 14,5 24,969 Sodium channel subunit beta-4 SULF2 Q8IWU5-2;Q8IWU5 4 4 5,3 100,16 Extracellular sulfatase Sulf-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CNTN4 Q8IWV2;Q8IWV2- 25 7 36,5 113,45 Contactin-4 4;Q8IWV2-2 CNTN4 Q8IWV2-3 18 1 40 76,526 Contactin-4 SCUBE1 Q8IWY4 8 7 13,8 107,91 , CUB and EGF-like domain-containing protein 1 FAM20C Q8IXL6;Q8IXL6-2 15 14 35,4 66,234 Extracellular serine/threonine protein kinase FAM20C CMIP Q8IY22 1 1 2,6 86,33 C-Maf-inducing protein TMEFF1 Q8IYR6-2;Q8IYR6 1 1 4,7 37,757 Tomoregulin-1 OSCAR Q8IYS5-6;Q8IYS5- 2 2 11,9 27,629 Osteoclast-associated 2;Q8IYS5-3;Q8IYS5- immunoglobulin-like receptor 4;Q8IYS5- 5;Q8IYS5;Q8IYS5-7 CHPF Q8IZ52- 2 2 4,9 68,34 Chondroitin sulfate synthase 2 4;Q8IZ52;Q8IZ52-2 KIAA0319L Q8IZA0- 6 6 7,6 109,75 Dyslexia-associated protein KIAA0319- 2;Q8IZA0;Q8IZA0-3 like protein UNC5B Q8IZJ1-2;Q8IZJ1 3 3 4,6 102,43 Netrin receptor UNC5B CPAMD8 Q8IZJ3-2;Q8IZJ3 12 12 11,1 199,17 C3 and PZP-like alpha-2-macroglobulin domain-containing protein 8 HS6ST3 Q8IZP7 11 11 29,3 54,843 Heparan-sulfate 6-O-sulfotransferase 3 CACNA2D3 Q8IZS8;Q8IZS8- 17 17 21,4 123,01 Voltage-dependent calcium channel 2;Q8IZS8-3 subunit alpha-2/delta-3;Voltage- dependent calcium channel subunit alpha-2-3;Voltage-dependent calcium channel subunit delta-3 NLGN4X;NLGN4Y Q8N0W4;Q8N0W4- 8 5 17,5 91,914 Neuroligin-4, X-linked;Neuroligin-4, Y- 2;Q8NFZ3-2;Q8NFZ3 linked

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SHISA5 Q8N114- 4 4 17,2 22,367 Protein shisa-5 2;Q8N114;Q8N114-5

CADM3 Q8N126;Q8N126- 12 12 39,9 43,299 Cell adhesion molecule 3 2;Q8N126-3 FAM177A1 Q8N128;Q8N128-2 2 2 10,3 23,757 Protein FAM177A1 CNPY4 Q8N129 3 3 17,7 28,309 Protein canopy homolog 4 LILRA2 Q8N149-3;Q8N149- 3 3 12 46,805 Leukocyte immunoglobulin-like 4;Q8N149-2;Q8N149 receptor subfamily A member 2

LYPD1 Q8N2G4- 2 2 39,3 9,4231 Ly6/PLAUR domain-containing protein 4;Q8N2G4;Q8N2G4- 1 3;Q8N2G4-2 NLGN1 Q8N2Q7-2;Q8N2Q7 6 4 10,7 91,999 Neuroligin-1

LTBP4 Q8N2S1-2;Q8N2S1- 28 28 27,2 165,74 Latent-transforming growth factor 3;Q8N2S1;Q8N2S1-4 beta-binding protein 4

EHBP1L1 Q8N3D4 1 1 1,3 161,85 EH domain-binding protein 1-like protein 1 FAM19A2 Q8N3H0 1 1 10,7 14,62 Protein FAM19A2 CADM2 Q8N3J6- 11 11 47,3 44,423 Cell adhesion molecule 2 2;Q8N3J6;Q8N3J6- 3;Q8N3J6-4;Q8N3J6-5

GALNT15 Q8N3T1 8 8 15,3 73,063 Polypeptide N- acetylgalactosaminyltransferase 15 TMEM132C Q8N3T6 24 24 32,3 121,79 Transmembrane protein 132C PRSS35 Q8N3Z0 1 1 3,4 47,097 Inactive serine protease 35

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GALNT16 Q8N428-2;Q8N428 5 5 10,3 60,971 Polypeptide N- acetylgalactosaminyltransferase 16 CPXM2 Q8N436 10 9 16,5 85,869 Inactive carboxypeptidase-like protein X2 SFRP1 Q8N474 3 3 12,1 35,385 Secreted frizzled-related protein 1 FSTL5 Q8N475- 24 22 34,2 95,622 Follistatin-related protein 5 2;Q8N475;Q8N475-3

GALNT4 Q8N4A0;Q8N4A0- 4 3 7,4 66,665 Polypeptide N- 2;Q8IXK2 acetylgalactosaminyltransferase 4 OXR1 Q8N573-7;Q8N573- 2 2 13,9 24,467 Oxidation resistance protein 1 4;Q8N573-6;Q8N573- 2;Q8N573-5;Q8N573- 8;Q8N573

DPP10 Q8N608-4;Q8N608- 4 3 5 85,479 Inactive dipeptidyl peptidase 10 2;Q8N608;Q8N608-3

IGSF1 Q8N6C5- 7 7 6,6 147,97 Immunoglobulin superfamily member 2;Q8N6C5;Q8N6C5-4 1

LILRA3 Q8N6C8;Q8N6C8- 3 2 9,6 47,471 Leukocyte immunoglobulin-like 3;Q8N6C8-2;O75019- receptor subfamily A member 3 2;O75019

ADAMTSL1 Q8N6G6-2;Q8N6G6- 1 1 2,5 48,764 ADAMTS-like protein 1 1;Q8N6G6-4;Q8N6G6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LRRC17 Q8N6Y2-2;Q8N6Y2 1 1 3,5 36,273 Leucine-rich repeat-containing protein 17 DCBLD1 Q8N8Z6-2;Q8N8Z6 2 2 4,6 59,195 Discoidin, CUB and LCCL domain- containing protein 1 LRTM2 Q8N967 5 5 20,8 41,157 Leucine-rich repeat and transmembrane domain-containing protein 2 SYT2 Q8N9I0 5 3 11,5 46,872 Synaptotagmin-2 DRAXIN Q8NBI3 3 3 9,5 38,65 Draxin XXYLT1 Q8NBI6;Q8NBI6- 8 8 27,5 43,806 Xyloside xylosyltransferase 1 3;Q8NBI6-2 GOLM1 Q8NBJ4-2;Q8NBJ4 18 18 51,7 44,272 Golgi membrane protein 1 SUMF2 Q8NBJ7- 2 2 14,7 23,902 Sulfatase-modifying factor 2 5;Q8NBJ7;Q8NBJ7- 2;Q8NBJ7-4;Q8NBJ7-3

SUMF1 Q8NBK3-2;Q8NBK3- 1 1 6,7 31,9 Sulfatase-modifying factor 1 4;Q8NBK3- 5;Q8NBK3;Q8NBK3-3

PCSK9 Q8NBP7;Q8NBP7-2 10 10 23,7 74,285 Proprotein convertase subtilisin/kexin type 9 TXNDC5 Q8NBS9-2;Q8NBS9 3 3 9,3 36,177 Thioredoxin domain-containing protein 5 UXS1 Q8NBZ7;Q8NBZ7- 3 3 7,6 47,576 UDP-glucuronic acid decarboxylase 1 2;Q8NBZ7-3 FAM134A Q8NC44 1 1 4,6 57,829 Protein FAM134A PLA2G15 Q8NCC3;Q8NCC3-2 4 4 12,9 46,657 Group XV CHST14 Q8NCH0 4 4 13 42,996 Carbohydrate sulfotransferase 14

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GALNT6 Q8NCL4 10 10 21,2 71,158 Polypeptide N- acetylgalactosaminyltransferase 6 APOA1BP Q8NCW5-2;Q8NCW5 6 6 45,4 20,43 NAD(P)H-hydrate epimerase

GALNT11 Q8NCW6 2 2 3,6 68,918 Polypeptide N- acetylgalactosaminyltransferase 11 LFNG Q8NES3- 9 9 35,5 39,587 Beta-1,3-N- 3;Q8NES3;Q8NES3- acetylglucosaminyltransferase lunatic 2;Q8NES3-4 fringe MDGA1 Q8NFP4;Q8NFP4-2 9 9 16,8 105,79 MAM domain-containing glycosylphosphatidylinositol anchor protein 1 DNER Q8NFT8 7 7 15,6 78,474 Delta and Notch-like epidermal growth factor-related receptor SEMA6D Q8NFY4- 16 15 18,5 117,86 Semaphorin-6D 6;Q8NFY4;Q8NFY4- 8;Q8NFY4-3;Q8NFY4- 2;Q8NFY4-4;Q8NFY4- 5;Q8NFY4-7

NLGN2 Q8NFZ4 8 6 16,4 90,819 Neuroligin-2 CADM4 Q8NFZ8 12 12 44,6 42,785 Cell adhesion molecule 4 SVIP Q8NHG7 1 1 14,3 8,4426 Small VCP/p97-interacting protein LILRB4 Q8NHJ6- 3 3 7,2 49,227 Leukocyte immunoglobulin-like 2;Q8NHJ6;Q8NHJ6-3 receptor subfamily B member 4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LILRB1 Q8NHL6- 2 1 9,2 49,356 Leukocyte immunoglobulin-like 5;Q8NHL6;Q8NHL6- receptor subfamily B member 1 4;Q8NHL6-2;Q8NHL6-3

PLBD2 Q8NHP8;Q8NHP8-2 4 4 8,8 65,471 Putative -like 2;Putative phospholipase B-like 2 32 kDa form;Putative phospholipase B- like 2 45 kDa form MCFD2 Q8NI22-2;Q8NI22- 1 1 25,5 10,718 Multiple coagulation factor deficiency 3;Q8NI22 protein 2 PCDH19 Q8TAB3-3;Q8TAB3- 5 5 7,5 121,01 Protocadherin-19 2;Q8TAB3 VSTM2A Q8TAG5-2;Q8TAG5 5 5 38,5 27,181 V-set and transmembrane domain- containing protein 2A FIBIN Q8TAL6 2 2 11,4 24,273 Fin bud initiation factor homolog ERMN Q8TAM6;Q8TAM6-2 1 1 3,9 32,783 Ermin

NDNF Q8TB73 2 2 4,9 64,672 Protein NDNF ITFG1 Q8TB96 1 1 1,5 68,107 T-cell immunomodulatory protein FAM174A Q8TBP5 1 1 12,6 19,954 Membrane protein FAM174A NT5C Q8TCD5;Q8TCD5-2 2 2 20,4 23,382 5(3)-deoxyribonucleotidase, cytosolic type CD99L2 Q8TCZ2;Q8TCZ2- 7 7 38,5 27,986 CD99 antigen-like protein 2 2;Q8TCZ2-5;Q8TCZ2- 6;Q8TCZ2-3

NETO1 Q8TDF5-1;Q8TDF5- 4 4 27,6 17,669 Neuropilin and tolloid-like protein 1 2;Q8TDF5 HAVCR2 Q8TDQ0-2;Q8TDQ0 3 3 37,3 16,149 Hepatitis A virus cellular receptor 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GNPDA2 Q8TDQ7-3;Q8TDQ7- 2 1 10 29,173 Glucosamine-6-phosphate isomerase 2 2;Q8TDQ7;Q8TDQ7- 4;Q8TDQ7-5 FAT3 Q8TDW7- 6 6 1,7 501,97 Protocadherin Fat 3 3;Q8TDW7;Q8TDW7-2

IGDCC4 Q8TDY8 3 3 3,3 134,21 Immunoglobulin superfamily DCC subclass member 4 ADAMTS16 Q8TE57-2;Q8TE57 2 2 2,3 119,51 A disintegrin and metalloproteinase with thrombospondin motifs 16 DTD1 Q8TEA8 2 2 11 23,423 D-tyrosyl-tRNA(Tyr) deacylase 1 SNED1 Q8TER0;Q8TER0- 16 16 18 152,2 Sushi, nidogen and EGF-like domain- 4;Q8TER0-5;Q8TER0-3 containing protein 1

WFIKKN2 Q8TEU8;Q96NZ8 18 18 33,7 63,941 WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 TSKU Q8WUA8 2 2 7,1 37,807 Tsukushin CEMIP Q8WUJ3;Q8WUJ3-2 21 21 21,2 153 Cell migration-inducing and hyaluronan-binding protein PDCD6IP Q8WUM4;Q8WUM4- 3 3 5,1 96,022 Programmed cell death 6-interacting 2;Q8WUM4-3 protein CANT1 Q8WVQ1- 14 14 56 38,945 Soluble calcium-activated nucleotidase 3;Q8WVQ1;Q8WVQ1-2 1

SELM Q8WWX9 4 4 49,7 16,231 Selenoprotein M IGFBPL1 Q8WX77 5 5 38,1 29,005 Insulin-like growth factor-binding protein-like 1 SCG3 Q8WXD2;Q8WXD2-2 36 36 72,2 53,005 Secretogranin-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SYNE2 Q8WXH0;Q8WXH0- 3 3 0,5 796,43 Nesprin-2 2;Q8WXH0-7;Q8WXH0- 13 CACNG8 Q8WXS5 2 2 13,4 43,312 Voltage-dependent calcium channel gamma-8 subunit SORCS1 Q8WY21- 13 12 15,2 129,14 VPS10 domain-containing receptor 4;Q8WY21;Q8WY21- SorCS1 3;Q8WY21-2 CNTNAP5 Q8WYK1 9 8 7,8 145,62 Contactin-associated protein-like 5 ROBO4 Q8WZ75-3;Q8WZ75- 3 3 6,4 75,281 Roundabout homolog 4 2;Q8WZ75

POMGNT1 Q8WZA1;Q8WZA1-2 28 28 47,3 75,251 Protein O-linked-mannose beta-1,2-N- acetylglucosaminyltransferase 1 ST8SIA4 Q92187-2;Q92187 1 1 11,3 19,26 CMP-N-acetylneuraminate-poly-alpha- 2,8-sialyltransferase SMPDL3A Q92484;Q92484-2 6 6 20,5 51,26 -like phosphodiesterase 3a SMPDL3B Q92485-2;Q92485 7 7 29,8 41,689 Acid sphingomyelinase-like phosphodiesterase 3b CFHR4 Q92496- 5 2 12 65,221 Complement factor H-related protein 2;Q92496;Q92496-3 4

DDX1 Q92499-3;Q92499- 1 1 3,1 68,712 ATP-dependent RNA DDX1 2;Q92499 FAM3C Q92520 16 16 67,8 24,68 Protein FAM3C NCSTN Q92542-2;Q92542 4 4 6,1 76,743 Nicastrin SPOCK2 Q92563;Q92563-2 16 16 48,3 46,779 Testican-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SLC9A6 Q92581- 1 1 1,8 72,259 Sodium/hydrogen exchanger 6 3;Q92581;Q92581-2

PXDN Q92626;Q92626-2 5 5 5 165,27 Peroxidasin homolog SORL1 Q92673 50 50 31,7 248,42 Sortilin-related receptor NRGN Q92686 1 1 19,2 7,6184 Neurogranin;NEUG(55-78) PVRL2 Q92692-2;Q92692 7 7 20 51,359 Nectin-2 PTPRU Q92729-3;Q92729- 2 2 2,2 160,79 Receptor-type tyrosine-protein 2;Q92729-4;Q92729 phosphatase U

HTRA1 Q92743 10 10 29,4 51,286 Serine protease HTRA1 TNR Q92752;Q92752-2 26 26 27,5 149,56 Tenascin-R FRZB Q92765 6 6 27,1 36,254 Secreted frizzled-related protein 3 STAM Q92783-2;Q92783 1 1 4 44,971 Signal transducing adapter molecule 1 GGH Q92820 13 13 39,3 35,964 Gamma-glutamyl hydrolase NRCAM Q92823- 42 42 46 136,61 Neuronal cell adhesion molecule 2;Q92823;Q92823- 5;Q92823-3;Q92823- 6;Q92823-4

PCSK5 Q92824-2;Q92824 1 1 1,4 101,65 Proprotein convertase subtilisin/kexin type 5 NELL1 Q92832-2;Q92832 4 4 8,7 84,377 Protein kinase C-binding protein NELL1 EDA Q92838-9;Q92838- 1 1 4,9 40,75 Ectodysplasin-A;Ectodysplasin-A, 3;Q92838 membrane form;Ectodysplasin-A, secreted form SEMA4D Q92854;Q92854-2 4 4 7,4 96,149 Semaphorin-4D NEO1 Q92859-3;Q92859- 37 37 37,2 154,3 Neogenin 2;Q92859-4;Q92859

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] KLK6 Q92876;Q92876-2 11 11 72,1 26,855 Kallikrein-6 UFD1L Q92890- 2 2 10,5 29,901 Ubiquitin fusion degradation protein 1 3;Q92890;Q92890-1 homolog

GLG1 Q92896;Q92896- 12 12 13,9 134,55 Golgi apparatus protein 1 2;Q92896-3 PTPRN2 Q92932;Q92932- 19 2 29,6 111,27 Receptor-type tyrosine-protein 4;Q92932-3 phosphatase N2 PTPRN2 Q92932-2 18 1 27,6 108,05 Receptor-type tyrosine-protein phosphatase N2 PRG4 Q92954-3;Q92954-4 21 2 18,8 141,1 Proteoglycan 4;Proteoglycan 4 C- terminal part TNFRSF14 Q92956;Q92956-2 4 4 28,6 30,391 Tumor necrosis factor receptor superfamily member 14 EXT2 Q93063;Q93063- 11 11 20,2 82,254 Exostosin-2 2;Q93063-3 RNASE6 Q93091 3 3 30,7 17,196 Ribonuclease K6 C19orf10 Q969H8 3 3 15,6 18,795 UPF0556 protein C19orf10 IGSF8 Q969P0- 13 13 30,8 55,807 Immunoglobulin superfamily member 3;Q969P0;Q969P0-2 8

WBP2 Q969T9 5 5 23,4 28,087 WW domain-binding protein 2 RELT Q969Z4 3 3 12,8 46,091 Tumor necrosis factor receptor superfamily member 19L MRGPRF Q96AM1 1 1 4,1 38,171 Mas-related G-protein coupled receptor member F ESAM Q96AP7 5 5 16,9 41,176 Endothelial cell-selective adhesion molecule

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PBXIP1 Q96AQ6- 12 12 20,5 77,683 Pre-B-cell leukemia transcription 2;Q96AQ6;Q96AQ6-3 factor-interacting protein 1

RGMA Q96B86- 10 10 42,2 47,511 Repulsive guidance molecule A 3;Q96B86;Q96B86-4

SARAF Q96BY9 4 4 16,5 36,975 Store-operated calcium entry- associated regulatory factor PLD4 Q96BZ4 7 7 16,4 55,626 Phospholipase D4 EFHD2;EFHD1 Q96C19;Q9BUP0-2 4 2 20,8 26,697 EF-hand domain-containing protein D2;EF-hand domain-containing protein D1 CTHRC1 Q96CG8- 3 3 15,3 24,77 Collagen triple helix repeat-containing 3;Q96CG8;Q96CG8-2 protein 1

PLEKHB2 Q96CS7-5;Q96CS7- 2 2 15,2 20,375 Pleckstrin domain- 3;Q96CS7;Q96CS7- containing family B member 2 6;Q96CS7-2;Q96CS7-4

NTNG2 Q96CW9-2;Q96CW9 2 2 8,3 47,491 Netrin-G2

KCTD12 Q96CX2;Q68DU8 6 6 31,1 35,7 BTB/POZ domain-containing protein KCTD12 C10orf35 Q96D05;Q96D05-2 1 1 10,7 13,238 Uncharacterized protein C10orf35 RCN3 Q96D15 3 3 14,6 37,493 Reticulocalbin-3 SHISA4 Q96DD7 1 1 4,6 21,522 Protein shisa-4 TBC1D31 Q96DN5 2 2 1,4 124,19 TBC1 domain family member 31 ERLEC1 Q96DZ1-2;Q96DZ1- 1 1 4,2 48,882 Endoplasmic reticulum lectin 1 3;Q96DZ1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CCDC126 Q96EE4 2 1 14,3 15,668 Coiled-coil domain-containing protein 126 ARSG Q96EG1 1 1 3,6 57,06 Arylsulfatase G C1GALT1C1 Q96EU7 2 2 9,4 36,382 C1GALT1-specific chaperone 1 CNRIP1 Q96F85-2;Q96F85 2 2 27,3 14,224 CB1 -interacting protein 1 LINGO1 Q96FE5-2;Q96FE5 11 10 23,8 69,145 Leucine-rich repeat and immunoglobulin-like domain- containing nogo receptor-interacting protein 1 PIK3IP1 Q96FE7-4;Q96FE7- 8 8 37,6 18,491 Phosphoinositide-3-kinase-interacting 2;Q96FE7;Q96FE7-5 protein 1

DYNLL2 Q96FJ2;P63167 4 4 50,6 10,35 Dynein light chain 2, cytoplasmic OTUB1 Q96FW1;Q96FW1-2 2 2 9,6 31,284 Ubiquitin thioesterase OTUB1

Q96G97-4 1 1 3,9 51,158 PDXP Q96GD0 2 2 7,1 31,698 Pyridoxal phosphate phosphatase BCAN Q96GW7;Q96GW7-2 27 26 46 99,117 core protein

PDLIM5 Q96HC4;Q96HC4- 2 2 4,9 63,944 PDZ and LIM domain protein 5 3;Q96HC4-2;Q96HC4- 7;Q96HC4-4;Q96HC4-6

CRELD1 Q96HD1-2;Q96HD1 14 14 53,6 45,941 Cysteine-rich with EGF-like domain protein 1 SFRP2 Q96HF1 3 3 12,5 33,49 Secreted frizzled-related protein 2 DDRGK1 Q96HY6-2;Q96HY6 1 1 6,1 35,475 DDRGK domain-containing protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] KAZALD1 Q96I82-2;Q96I82 1 1 7,9 26,525 Kazal-type serine protease inhibitor domain-containing protein 1 IGSF21 Q96ID5 7 7 21,4 51,835 Immunoglobulin superfamily member 21 ABHD14B Q96IU4 2 2 12,9 22,345 Alpha/beta hydrolase domain- containing protein 14B CPB2 Q96IY4;Q96IY4- 14 14 39,7 48,424 2;CON__Q2KIG3 LRIG1 Q96JA1-2;Q96JA1 5 5 6,4 116,38 Leucine-rich repeats and immunoglobulin-like domains protein 1 ST6GAL2 Q96JF0;Q96JF0-2 7 7 16,8 60,157 Beta-galactoside alpha-2,6- sialyltransferase 2 CDHR1 Q96JP9;Q96JP9-2 6 6 10,7 93,594 Cadherin-related family member 1 DCHS1 Q96JQ0 9 9 5 346,18 Protocadherin-16 MEGF10 Q96KG7;Q96KG7-2 13 13 17,1 122,2 Multiple epidermal growth factor-like domains protein 10 CNDP1 Q96KN2 30 30 64,7 56,705 Beta-Ala-His dipeptidase CNDP2 Q96KP4-2;Q96KP4 2 2 6,1 43,833 Cytosolic non-specific dipeptidase LMLN Q96KR4;Q96KR4-3 1 1 1,8 73,567 -like peptidase FAM19A4 Q96LR4 2 2 20,7 15,682 Protein FAM19A4 FAM20A Q96MK3 3 2 8,9 61,416 Protein FAM20A HS6ST2 Q96MM7-2;Q96MM7- 1 1 2,6 53,436 Heparan-sulfate 6-O-sulfotransferase 2 3;Q96MM7;Q96MM7-4

KREMEN1 Q96MU8- 2 2 9 50,176 Kremen protein 1 3;Q96MU8;Q96MU8-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LRFN5 Q96NI6 1 1 1,4 79,444 Leucine-rich repeat and fibronectin type-III domain-containing protein 5 CLIC6 Q96NY7-2;Q96NY7 2 2 4,5 70,995 Chloride intracellular channel protein 6 PRAP1 Q96NZ9- 2 2 26,8 16,331 Proline-rich acidic protein 1 4;Q96NZ9;Q96NZ9- 3;Q96NZ9-2 COL21A1 Q96P44-3;Q96P44 6 6 9 99,067 Collagen alpha-1(XXI) chain OLFM3 Q96PB7-4;Q96PB7- 2 2 14 25,089 Noelin-3 2;Q96PB7- 3;Q96PB7;Q96PB7- 6;Q96PB7-5 DCBLD2 Q96PD2;Q96PD2-2 1 1 2,6 85,034 Discoidin, CUB and LCCL domain- containing protein 2 PGLYRP2 Q96PD5;Q96PD5- 16 16 48,1 62,216 N-acetylmuramoyl-L-alanine amidase 2;CON__ENSEMBL:ENS BTAP00000016285

SLITRK1 Q96PX8 17 17 34,9 77,734 SLIT and NTRK-like protein 1 CSMD1 Q96PZ7- 3 3 1,7 370,31 CUB and sushi domain-containing 2;Q96PZ7;Q96PZ7- protein 1 4;Q96PZ7-3 HHIP Q96QV1-2;Q96QV1 2 2 6,6 36,373 Hedgehog-interacting protein GAL3ST4 Q96RP7-2;Q96RP7 1 1 2,1 46,587 -3-O-sulfotransferase 4 HMCN1 Q96RW7- 38 38 9,7 600,09 Hemicentin-1 2;Q96RW7;Q96RW7-3

PEBP4 Q96S96 8 8 51,1 25,733 Phosphatidylethanolamine-binding protein 4 CPXM1 Q96SM3 6 6 14,9 81,667 Probable carboxypeptidase X1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] RMDN3 Q96TC7;Q96TC7-2 7 7 17,2 52,118 Regulator of microtubule dynamics protein 3 HBEGF Q99075 1 1 5,3 23,067 Proheparin-binding EGF-like growth factor;Heparin-binding EGF-like growth factor SCN2A Q99250-2;Q99250 2 1 1,6 227,97 Sodium channel protein type 2 subunit alpha TBCB Q99426-2;Q99426 1 1 13 21,801 Tubulin-folding cofactor B NELL2 Q99435- 34 34 57,8 91,166 Protein kinase C-binding protein NELL2 4;Q99435;Q99435- 2;Q99435-3 CDC5L Q99459 2 2 2,7 92,25 Cell division cycle 5-like protein PARK7 Q99497 12 12 73,5 19,891 Protein DJ-1 NEU1 Q99519 5 5 22,7 45,467 Sialidase-1 SORT1 Q99523;Q99523-2 10 10 15,5 92,067 Sortilin LGMN Q99538- 3 3 13,6 42,947 Legumain 2;Q99538;Q99538-3

MMP19 Q99542;Q99542-5 2 2 6,7 57,356 Matrix metalloproteinase-19 SERPINI1 Q99574 18 18 53,4 46,426 Neuroserpin S100A13 Q99584 2 2 21,4 11,471 Protein S100-A13 OSMR Q99650-2;Q99650 6 6 24,9 39,503 Oncostatin-M-specific receptor subunit beta CGREF1 Q99674;Q99674- 12 12 64,8 31,905 Cell growth regulator with EF hand 4;Q99674-5;Q99674- domain protein 1 2;Q99674-3

COL12A1 Q99715;Q99715- 41 41 18,1 333,14 Collagen alpha-1(XII) chain 4;Q99715-2 TIMP4 Q99727 5 5 23,7 25,502 Metalloproteinase inhibitor 4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] Q99729-3;Q99729-2 1 1 4,9 30,588

OLFM1 Q99784-5;Q99784- 7 7 20,5 52,814 Noelin 3;Q99784;Q99784- 4;Q99784-2 TSG101 Q99816 1 1 2,6 43,944 Tumor susceptibility gene 101 protein ATF6B Q99941-2;Q99941 7 7 9,6 76,411 Cyclic AMP-dependent transcription factor ATF-6 beta;Processed cyclic AMP-dependent transcription factor ATF-6 beta EGFL8 Q99944 2 2 11,9 32,262 Epidermal growth factor-like protein 8 PRRT1 Q99946 2 2 8,5 31,43 Proline-rich transmembrane protein 1 RARRES2 Q99969 4 4 42,3 18,617 Retinoic acid receptor responder protein 2 MYOC Q99972 6 6 15,3 56,971 Myocilin;Myocilin, N-terminal fragment;Myocilin, C-terminal fragment OMD Q99983 7 7 26,8 49,492 Osteomodulin SEMA3C Q99985;Q99985-2 7 7 13,8 85,206 Semaphorin-3C SPOCK3 Q9BQ16;Q9BQ16- 9 1 31,2 49,428 Testican-3 2;Q9BQ16-4;Q9BQ16- 7;Q9BQ16-6;Q9BQ16-5

PDCD1LG2 Q9BQ51-3;Q9BQ51- 1 1 6,6 20,744 Programmed cell death 1 ligand 2 2;Q9BQ51 SYT3 Q9BQG1 1 1 1,9 63,303 Synaptotagmin-3 PRSS27 Q9BQR3 1 1 3,4 31,939 Serine protease 27

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HEPH Q9BQS7- 10 10 11,8 130,38 Hephaestin 2;Q9BQS7;Q9BQS7- 3;Q9BQS7-4 CLSTN3 Q9BQT9;Q9BQT9-2 12 12 18 106,1 Calsyntenin-3 CORO1B Q9BR76 1 1 2 54,234 Coronin-1B TXNDC17 Q9BRA2 5 5 53,7 13,941 Thioredoxin domain-containing protein 17 CPPED1 Q9BRF8- 3 3 18 19,035 Serine/threonine-;Q9BRF8;Q9BRF8-3 CPPED1

MXRA8 Q9BRK3- 5 5 15 47,971 Matrix-remodeling-associated protein 3;Q9BRK3;Q9BRK3- 8 2;Q9BRK3-4 SDF4 Q9BRK5;Q9BRK5- 11 11 43,6 41,806 45 kDa calcium-binding protein 6;Q9BRK5-2;Q9BRK5- 4;Q9BRK5-3;Q9BRK5-5

ERP44 Q9BS26 6 6 17 46,971 Endoplasmic reticulum resident protein 44 RTBDN Q9BSG5;Q9BSG5- 4 4 23,6 24,615 Retbindin 3;Q9BSG5-2 CNPY3 Q9BT09 5 5 23 30,748 Protein canopy homolog 3 SYT11 Q9BT88 2 2 6,5 48,296 Synaptotagmin-11 FUCA2 Q9BTY2;Q9BTY2-2 12 12 30,6 54,066 Plasma alpha-L-fucosidase CHRDL1 Q9BU40-2;Q9BU40- 13 13 38,5 51,425 Chordin-like protein 1 4;Q9BU40- 5;Q9BU40;Q9BU40- 6;Q9BU40-3 SPON2 Q9BUD6 6 6 28,1 35,846 Spondin-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ABHD14A Q9BUJ0 4 4 18,5 29,764 Alpha/beta hydrolase domain- containing protein 14A MENT Q9BUN1;Q9BUN1-2 3 3 11,1 36,769 Protein MENT

TMED9 Q9BVK6 3 2 25,1 27,277 Transmembrane emp24 domain- containing protein 9 TPPP3 Q9BW30 1 1 8 18,985 Tubulin polymerization-promoting protein family member 3 COLEC11 Q9BWP8-8;Q9BWP8- 2 2 13,7 21,589 Collectin-11 7;Q9BWP8-6;Q9BWP8- 5;Q9BWP8-4;Q9BWP8- 3;Q9BWP8-2;Q9BWP8- 9;Q9BWP8;Q9BWP8-10

FAIM2 Q9BWQ8 3 3 13,6 35,109 Protein lifeguard 2 CHID1 Q9BWS9- 5 5 15,2 41,677 Chitinase domain-containing protein 1 3;Q9BWS9;Q9BWS9-2

BOC Q9BWV1;Q9BWV1- 6 6 9,1 121,06 Brother of CDO 3;Q9BWV1-2 JAM3 Q9BX67-2;Q9BX67 5 5 27,8 29,223 Junctional adhesion molecule C C1QTNF5 Q9BXJ0 3 3 16,9 25,298 Complement C1q tumor necrosis factor-related protein 5 C1QTNF1 Q9BXJ1;Q9BXJ1-2 2 2 13,9 31,742 Complement C1q tumor necrosis factor-related protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] C1QTNF4 Q9BXJ3 7 7 36,2 35,256 Complement C1q tumor necrosis factor-related protein 4 C1QTNF3 Q9BXJ4- 3 3 18,5 35,183 Complement C1q tumor necrosis 3;Q9BXJ4;Q9BXJ4-2 factor-related protein 3 ASPN Q9BXN1 1 1 2,6 43,417 Asporin CLEC7A Q9BXN2-5;Q9BXN2- 1 1 7,1 19,217 C-type lectin domain family 7 member 2;Q9BXN2 A PAPPA2 Q9BXP8;Q9BXP8-2 8 8 9,7 198,54 Pappalysin-2 CFHR5 Q9BXR6 4 3 9 64,419 Complement factor H-related protein 5 TMEM59 Q9BXS4 4 4 20,7 36,223 Transmembrane protein 59 EMILIN2 Q9BXX0 9 9 13,3 115,69 EMILIN-2 CADM1 Q9BY67-5;Q9BY67- 13 13 44,2 45,623 Cell adhesion molecule 1 2;Q9BY67;Q9BY67- 4;Q9BY67-3 ANGPTL4 Q9BY76;Q9BY76- 4 4 17,2 45,214 Angiopoietin-related protein 4 2;Q9BY76-3 MFRP Q9BY79-2;Q9BY79 5 5 13,7 48,918 Membrane frizzled-related protein FUT8 Q9BYC5;Q9BYC5- 4 4 7,3 66,515 Alpha-(1,6)-fucosyltransferase 2;Q9BYC5-3 SEZ6L Q9BYH1-3;Q9BYH1- 11 10 26,9 87,592 Seizure 6-like protein 7;Q9BYH1- 6;Q9BYH1;Q9BYH1- 2;Q9BYH1-5;Q9BYH1-4

FGFBP2 Q9BYJ0 3 3 20,2 24,581 Fibroblast growth factor-binding protein 2 HELZ2 Q9BYK8-2;Q9BYK8- 1 1 0,4 231,67 Helicase with zinc finger domain 2 4;Q9BYK8

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CNTNAP3;CNTNAP3B Q9BZ76;Q9BZ76- 6 4 5,9 140,69 Contactin-associated protein-like 2;Q96NU0;Q96NU0- 3;Contactin-associated protein-like 3B 3;Q96NU0-2 ABCA2 Q9BZC7- 4 4 2,8 230,56 ATP-binding cassette sub-family A 2;Q9BZC7;Q9BZC7-3 member 2

LYNX1 Q9BZG9;Q9BZG9-3 2 1 19,1 14,026 Ly-6/neurotoxin-like protein 1 LYNX1 Q9BZG9-2 3 2 25,9 12,641 Ly-6/neurotoxin-like protein 1 ULBP2 Q9BZM5;Q6H3X3- 6 6 26,4 27,368 NKG2D ligand 2 2;Q5VY80;Q6H3X3 RTN4R Q9BZR6 13 13 38,5 50,707 Reticulon-4 receptor IMPG2 Q9BZV3 1 1 1,5 138,62 Interphotoreceptor matrix proteoglycan 2 SIGLEC1 Q9BZZ2-2;Q9BZZ2- 1 1 0,9 175,72 3;Q9BZZ2 CNTNAP4 Q9C0A0;Q9C0A0-2 30 28 35,7 145,27 Contactin-associated protein-like 4 SEMA4C Q9C0C4 4 4 6,8 92,622 Semaphorin-4C YIPF3 Q9GZM5 2 2 6 38,247 Protein YIPF3;Protein YIPF3, 36 kDa form III TINAGL1 Q9GZM7;Q9GZM7-3 2 2 5,8 52,387 Tubulointerstitial nephritis antigen-like

PDGFD Q9GZP0-2;Q9GZP0 4 4 14,8 42,166 Platelet-derived growth factor D;Platelet-derived growth factor D, latent form;Platelet-derived growth factor D, receptor-binding form NRSN2 Q9GZP1 1 1 7,4 21,983 Neurensin-2 PITHD1 Q9GZP4-2;Q9GZP4 5 5 33,3 24,121 PITH domain-containing protein 1 NIF3L1 Q9GZT8- 5 5 18,6 38,983 Putative GTP cyclohydrolase 1 type 2 2;Q9GZT8;Q9GZT8-3 NIF3L1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MCOLN1 Q9GZU1 1 1 2,6 65,022 Mucolipin-1 PEG3 Q9GZU2-2;Q9GZU2- 2 2 2,3 165,96 Paternally-expressed gene 3 protein 4;Q9GZU2;Q9GZU2-3

HAPLN2 Q9GZV7 3 3 13,8 37,775 Hyaluronan and proteoglycan link protein 2 CHST6;CHST5 Q9GZX3;Q9GZS9;Q9GZ 2 2 5,8 44,098 Carbohydrate sulfotransferase S9-2 6;Carbohydrate sulfotransferase 5 TWSG1 Q9GZX9;Q9GZX9-2 5 5 28,7 25,017 Twisted gastrulation protein homolog 1 LHPP Q9H008;Q9H008-2 4 4 25,9 29,165 Phospholysine phosphohistidine inorganic pyrophosphate phosphatase FAM107B Q9H098;Q9H098-2 1 1 9,9 15,558 Protein FAM107B TOLLIP Q9H0E2;Q9H0E2-2 3 3 13,9 30,281 Toll-interacting protein FXYD6 Q9H0Q3;Q9H0Q3-2 2 2 15,8 10,542 FXYD domain-containing transport regulator 6 HDHD2 Q9H0R4-2;Q9H0R4 3 3 24,9 18,533 Haloacid dehalogenase-like hydrolase domain-containing protein 2 C11orf54 Q9H0W9-3;Q9H0W9- 1 1 6,4 29,491 Ester hydrolase C11orf54 2;Q9H0W9

NAPB Q9H115-3;Q9H115- 3 2 22,5 23,403 Beta-soluble NSF attachment protein 2;Q9H115 SLITRK2 Q9H156-2;Q9H156 5 4 10,6 82,694 SLIT and NTRK-like protein 2 CDH19 Q9H159-2;Q9H159 2 2 5,3 55,383 Cadherin-19 SIL1 Q9H173 6 6 16,1 52,084 Nucleotide exchange factor SIL1 XYLT2 Q9H1B5;Q9H1B5-2 2 2 4,4 96,766 Xylosyltransferase 2 MEGF9 Q9H1U4 9 9 15,3 62,983 Multiple epidermal growth factor-like domains protein 9 C2orf40 Q9H1Z8 4 4 18,2 17,183 Augurin

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CDH23 Q9H251-4;Q9H251- 7 1 2,8 365,54 Cadherin-23 2;Q9H251;Q9H251- 8;Q9H251-3;Q9H251-5

SH3BGRL3 Q9H299 1 1 20,4 10,438 SH3 domain-binding glutamic acid- rich-like protein 3 CXCL16 Q9H2A7 4 4 21,7 27,578 C-X-C motif chemokine 16 CHST8 Q9H2A9 1 1 3,3 48,834 Carbohydrate sulfotransferase 8 SEMA6A Q9H2E6;Q9H2E6-2 9 9 11,8 114,39 Semaphorin-6A CHRD Q9H2X0- 15 15 25,4 97,73 Chordin 5;Q9H2X0;Q9H2X0- 4;Q9H2X0-2;Q9H2X0-3

IFI27L2 Q9H2X8 1 1 10,8 12,41 Interferon alpha-inducible protein 27- like protein 2 SLC12A5 Q9H2X9-2;Q9H2X9 2 2 1,8 123,51 Solute carrier family 12 member 5 CRISPLD1 Q9H336 1 1 2,4 56,888 Cysteine-rich secretory protein LCCL domain-containing 1 CPVL Q9H3G5 11 11 29,8 54,163 Probable serine carboxypeptidase CPVL BOLA2 Q9H3K6-2;Q9H3K6 1 1 27,6 6,8417 BolA-like protein 2 SEMA4A Q9H3S1;Q9H3S1-2 3 3 4,2 83,573 Semaphorin-4A TMPRSS5 Q9H3S3 2 2 7,4 49,56 Transmembrane protease serine 5 SEMA6C Q9H3T2- 8 7 12,3 98,467 Semaphorin-6C 2;Q9H3T2;Q9H3T2-3

SEMA6B Q9H3T3-3;Q9H3T3 7 7 17,7 73,951 Semaphorin-6B FZD8 Q9H461 1 1 1,9 73,299 Frizzled-8 CUEDC2 Q9H467 1 1 4,9 32,009 CUE domain-containing protein 2 RNPEP Q9H4A4 2 2 4 72,595

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DPEP2 Q9H4A9-2;Q9H4A9 3 3 9,5 43,828 CLSTN2 Q9H4D0 13 13 15 107 Calsyntenin-2 SMOC1 Q9H4F8;Q9H4F8-2 6 6 18,7 48,162 SPARC-related modular calcium- binding protein 1 GLIPR2 Q9H4G4 2 2 14,3 17,218 Golgi-associated plant pathogenesis- related protein 1 POMK Q9H5K3 1 1 5,4 40,05 Protein O-mannose kinase SLITRK6 Q9H5Y7 5 4 7,8 95,109 SLIT and NTRK-like protein 6 IGFLR1 Q9H665 2 2 8,2 37,894 IGF-like family receptor 1 CLMP Q9H6B4 2 2 9,4 41,28 CXADR-like membrane protein CCDC134 Q9H6E4 1 1 8,3 26,56 Coiled-coil domain-containing protein 134 ANTXR1 Q9H6X2-4;Q9H6X2- 4 4 22,8 37,055 Anthrax toxin receptor 1 6;Q9H6X2-2;Q9H6X2- 5;Q9H6X2;Q9H6X2-3

C12orf49 Q9H741 5 5 39,5 23,594 UPF0454 protein C12orf49 CXorf36 Q9H7Y0;Q9H7Y0-2 6 6 25,2 48,554 Deleted in autism-related protein 1 MANSC1 Q9H8J5;Q9H8J5-2 8 8 21,3 46,81 MANSC domain-containing protein 1 MMRN2 Q9H8L6 11 11 19,3 104,41 Multimerin-2 GORASP2 Q9H8Y8- 1 1 4,4 39,768 Golgi reassembly-stacking protein 2 2;Q9H8Y8;Q9H8Y8-3

ERVMER34-1 Q9H9K5 2 2 4,8 63,546 Endogenous retrovirus group MER34 member 1 Env polyprotein FKRP Q9H9S5 4 4 13,3 54,567 Fukutin-related protein FN3KRP Q9HA64 1 1 4,2 34,412 Ketosamine-3-kinase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] LPHN3 Q9HAR2-3;Q9HAR2- 23 23 40 79,336 Latrophilin-3 2;Q9HAR2;Q9HAR2-4

SIAE Q9HAT2;Q9HAT2-2 8 8 18,4 58,314 Sialate O- EDA2R Q9HAV5;Q9HAV5- 2 2 8,8 32,758 Tumor necrosis factor receptor 3;Q9HAV5-2 superfamily member 27 SCPEP1 Q9HB40;Q9HB40-2 2 2 5,1 50,83 Retinoid-inducible serine carboxypeptidase LRTM1 Q9HBL6-2;Q9HBL6 1 1 5,9 29,651 Leucine-rich repeat and transmembrane domain-containing protein 1 SLC38A10 Q9HBR0;Q9HBR0- 15 15 24,8 119,76 Putative sodium-coupled neutral 3;Q9HBR0-2 amino acid transporter 10 CDH20 Q9HBT6 7 7 10,5 88,992 Cadherin-20 LRRC4 Q9HBW1 4 2 6,9 72,717 Leucine-rich repeat-containing protein 4 TMEM165 Q9HC07 1 1 7,7 34,905 Transmembrane protein 165 GLOD4 Q9HC38- 7 7 31,2 33,232 Glyoxalase domain-containing protein 2;Q9HC38;Q9HC38-3 4

PCDH9 Q9HC56-2;Q9HC56 17 17 21,9 132,25 Protocadherin-9 SPON1 Q9HCB6 19 19 33,5 90,973 Spondin-1 LRRC4C Q9HCJ2 4 1 5 71,949 Leucine-rich repeat-containing protein 4C ROBO2 Q9HCK4- 15 13 18,6 130,67 Roundabout homolog 2 2;Q9HCK4;Q9HCK4-3

PCDH18 Q9HCL0-2;Q9HCL0 3 3 3,1 126,02 Protocadherin-18 PLXNA4 Q9HCM2;Q9HCM2- 5 5 3,9 212,45 Plexin-A4 2;Q9HCM2-3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] GALNT9 Q9HCQ5 1 1 2,2 68,358 Polypeptide N- acetylgalactosaminyltransferase 9 CD248 Q9HCU0 5 5 6,5 80,858 Endosialin CELSR2 Q9HCU4 21 21 12,1 317,45 Cadherin EGF LAG seven-pass G-type receptor 2 TM9SF3 Q9HD45 4 4 6,5 67,887 Transmembrane 9 superfamily member 3 APMAP Q9HDC9-2;Q9HDC9 1 1 4,2 32,161 Adipocyte plasma membrane- associated protein EMC7 Q9NPA0 1 1 5,4 26,47 ER membrane protein complex subunit 7 A4GALT Q9NPC4 4 4 17 40,499 4-alpha- galactosyltransferase NRN1 Q9NPD7 4 4 36,6 15,333 Neuritin CD320 Q9NPF0;Q9NPF0-2 6 6 29,4 28,991 CD320 antigen PCDH12 Q9NPG4 2 2 2,4 128,99 Protocadherin-12 ACP6 Q9NPH0 1 1 2,6 48,854 phosphatase type 6 IL1RAP Q9NPH3- 11 11 31,5 41,018 Interleukin-1 receptor accessory 2;Q9NPH3;Q9NPH3- protein 5;Q9NPH3-3 SEMA4B Q9NPR2-2;Q9NPR2 11 11 22,3 81,402 Semaphorin-4B CD93 Q9NPY3 5 4 7,2 68,559 Complement component C1q receptor B3GAT2 Q9NPZ5 1 1 3,4 36,918 Galactosylgalactosylxylosylprotein 3- beta-glucuronosyltransferase 2 SCUBE2 Q9NQ36-3;Q9NQ36- 4 3 6,4 88,878 Signal peptide, CUB and EGF-like 2;Q9NQ36 domain-containing protein 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] SPINK5 Q9NQ38- 3 3 5,1 104,02 Serine protease inhibitor Kazal-type 2;Q9NQ38;Q9NQ38-3 5;Hemofiltrate peptide HF6478;Hemofiltrate peptide HF7665 CRTAC1 Q9NQ79- 24 24 53,5 70,433 Cartilage acidic protein 1 2;Q9NQ79;Q9NQ79-3

MANBAL Q9NQG1 1 1 25,9 9,467 Protein MANBAL XPNPEP1 Q9NQW7;Q9NQW7- 2 2 4,5 69,917 Xaa-Pro aminopeptidase 1 3;Q9NQW7- 2;Q9NQW7-4 NPDC1 Q9NQX5 4 4 19,7 34,516 Neural proliferation differentiation and control protein 1 ITM2C Q9NQX7;Q9NQX7- 7 7 36,7 30,223 Integral membrane protein 2C;CT-BRI3 2;Q9NQX7-3 MAN1C1 Q9NR34 6 6 14 70,91 Mannosyl-oligosaccharide 1,2-alpha- mannosidase IC MXRA5 Q9NR99 1 1 0,4 312,15 Matrix-remodeling-associated protein 5 PDGFC Q9NRA1-3;Q9NRA1- 2 2 17,4 18,784 Platelet-derived growth factor 2;Q9NRA1 C;Platelet-derived growth factor C, latent form;Platelet-derived growth factor C, receptor-binding form CHST12 Q9NRB3 7 7 21,3 48,414 Carbohydrate sulfotransferase 12 PCDHB16 Q9NRJ7;Q9Y5F1;Q9Y5F 3 2 5,4 84,982 Protocadherin beta-16 2;Q9Y5F0;Q9UN66

OLFML3 Q9NRN5- 11 11 33,4 43,588 Olfactomedin-like protein 3 2;Q9NRN5;Q9NRN5-3

CYTL1 Q9NRR1 3 3 28,7 15,577 Cytokine-like protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] HEBP1 Q9NRV9 1 1 8,5 21,097 -binding protein 1 C1GALT1 Q9NS00-2;Q9NS00 5 5 21 35,934 Glycoprotein-N-acetylgalactosamine 3- beta-galactosyltransferase 1 LTBP3 Q9NS15;Q9NS15-2 11 10 14 139,36 Latent-transforming growth factor beta-binding protein 3 THSD1 Q9NS62-3;Q9NS62- 1 1 3,3 47,863 Thrombospondin type-1 domain- 2;Q9NS62 containing protein 1 TNFRSF19 Q9NS68-2;Q9NS68 3 3 12,9 45,305 Tumor necrosis factor receptor superfamily member 19 GKN1 Q9NS71 1 1 7 21,999 Gastrokine-1 CA10 Q9NS85;Q9NS85-2 3 3 12,8 37,562 Carbonic anhydrase-related protein 10 SEMA3G Q9NS98 11 11 20,6 86,7 Semaphorin-3G ST6GALNAC1 Q9NSC7 6 6 14,5 68,563 Alpha-N-acetylgalactosaminide alpha- 2,6-sialyltransferase 1 EMILIN3 Q9NT22;Q9NT22-2 5 5 13,3 82,646 EMILIN-3 TENM2 Q9NT68-2;Q9NT68 3 3 1,3 292,26 Teneurin-2;Ten-2, soluble form;Ten-2 intracellular domain LRRC4B Q9NT99 14 11 22 76,433 Leucine-rich repeat-containing protein 4B CBLN4 Q9NTU7 5 5 32,8 21,808 Cerebellin-4 GINM1 Q9NU53 5 5 15,5 36,84 Glycoprotein integral membrane protein 1 FAM49B Q9NUQ9;Q9NUQ9-2 5 5 20,1 36,748 Protein FAM49B

AIG1 Q9NVV5-6;Q9NVV5- 1 1 11,2 15,342 Androgen-induced gene 1 protein 5;Q9NVV5-3;Q9NVV5- 4;Q9NVV5-2;Q9NVV5

IMPAD1 Q9NX62 15 15 50,7 38,681 Inositol monophosphatase 3

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] STAB1 Q9NY15;Q9NY15-2 15 15 9,8 275,48 Stabilin-1 DPP3 Q9NY33;Q9NY33- 10 10 20,6 82,588 Dipeptidyl peptidase 3 4;Q9NY33-2 CACNA2D2 Q9NY47-4;Q9NY47- 21 19 23,5 122,12 Voltage-dependent calcium channel 2;Q9NY47- subunit alpha-2/delta-2;Voltage- 3;Q9NY47;Q9NY47-5 dependent calcium channel subunit alpha-2-2;Voltage-dependent calcium channel subunit delta-2 OBP2A Q9NY56-3;Q9NY56 1 1 9,5 15,821 Odorant-binding protein 2a SCN3B Q9NY72 3 3 18,6 24,702 Sodium channel subunit beta-3 B3GNT2 Q9NY97-2;Q9NY97 10 10 30 45,484 UDP-GlcNAc:betaGal beta-1,3-N- acetylglucosaminyltransferase 2 CELSR3 Q9NYQ7;Q9NYQ7-2 3 3 1,4 358,18 Cadherin EGF LAG seven-pass G-type receptor 3 FAT2 Q9NYQ8 100 100 33,3 479,31 Protocadherin Fat 2 UGGT1 Q9NYU2-2;Q9NYU2 5 5 3,8 174,97 UDP-glucose:glycoprotein 1 CALY Q9NYX4 2 2 14,7 23,433 Neuron-specific vesicular protein calcyon ERAP1 Q9NZ08;Q9NZ08-2 20 20 27 107,23 Endoplasmic reticulum aminopeptidase 1 CISD1 Q9NZ45 1 1 12 12,199 CDGSH iron-sulfur domain-containing protein 1 PODXL2 Q9NZ53;Q9NZ53-2 5 5 13,7 65,075 Podocalyxin-like protein 2 STMN3 Q9NZ72-2;Q9NZ72 4 4 27,2 19,806 Stathmin-3 NLGN3 Q9NZ94-3;Q9NZ94- 6 4 11,8 89,537 Neuroligin-3 2;Q9NZ94 TREM2 Q9NZC2-2;Q9NZC2- 3 3 23,3 24,328 Triggering receptor expressed on 3;Q9NZC2 myeloid cells 2 AHSP Q9NZD4 1 1 12,7 11,84 Alpha-hemoglobin-stabilizing protein

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] CECR1 Q9NZK5;Q9NZK5-2 16 16 36,2 58,933 Adenosine deaminase CECR1 MAT2B Q9NZL9-3;Q9NZL9- 1 1 9,7 28,954 Methionine adenosyltransferase 2 4;Q9NZL9-2;Q9NZL9 subunit beta

IL1RAPL1 Q9NZN1 4 4 7 79,968 Interleukin-1 receptor accessory protein-like 1 C1RL Q9NZP8 8 8 26,9 53,498 Complement C1r subcomponent-like protein LRP1B Q9NZR2 16 16 4,7 515,49 Low-density lipoprotein receptor- related protein 1B CALML5 Q9NZT1 1 1 15,8 15,892 Calmodulin-like protein 5 FLRT3 Q9NZU0 4 4 7,7 73,003 Leucine-rich repeat transmembrane protein FLRT3 FLRT1 Q9NZU1 4 4 10,4 71,358 Leucine-rich repeat transmembrane protein FLRT1 CRIM1 Q9NZV1 7 7 12,6 113,74 Cysteine-rich motor neuron 1 protein;Processed cysteine-rich motor neuron 1 protein PTPLAD1 Q9P035-2;Q9P035 1 1 6,8 36,43 Very-long-chain (3R)-3-hydroxyacyl- CoA dehydratase 3 ADAM22 Q9P0K1-5;Q9P0K1- 20 20 35,5 96,636 Disintegrin and metalloproteinase 2;Q9P0K1;Q9P0K1- domain-containing protein 22 4;Q9P0K1-3 FRRS1L Q9P0K9 4 4 13,4 37,27 DOMON domain-containing protein FRRS1L VAPA Q9P0L0;Q9P0L0-2 3 2 11,2 27,893 Vesicle-associated membrane protein- associated protein A COX16 Q9P0S2 2 2 18,9 12,293 Cytochrome c oxidase assembly protein COX16 homolog, mitochondrial

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TMEM9 Q9P0T7 1 1 15,3 20,574 Transmembrane protein 9 NTM Q9P121-4;Q9P121- 13 12 48,2 39,226 Neurotrimin 3;Q9P121-2;Q9P121

CNTN3 Q9P232 19 19 22,6 112,88 Contactin-3 LRFN1 Q9P244 1 1 1,6 82,317 Leucine-rich repeat and fibronectin type III domain-containing protein 1 TENM3 Q9P273 3 3 1,6 300,95 Teneurin-3 PCDH10 Q9P2E7-2;Q9P2E7 13 13 18 97 Protocadherin-10 PTCHD2 Q9P2K9-2;Q9P2K9 2 2 3,1 103,77 Patched domain-containing protein 2 NRXN2 Q9P2S2 41 2 30,4 184,98 Neurexin-2 MRC2 Q9UBG0 14 14 15,1 166,67 C-type mannose receptor 2 DKK3 Q9UBP4 18 18 66 38,39 Dickkopf-related protein 3 EXTL2 Q9UBQ6 8 8 36,4 37,465 Exostosin-like 2;Processed exostosin- like 2 CTSZ Q9UBR2 7 7 25,7 33,868 DNAJB9 Q9UBS3 1 1 6,3 25,518 DnaJ homolog subfamily B member 9 DNAJB11 Q9UBS4 3 3 14 40,513 DnaJ homolog subfamily B member 11 GABBR1 Q9UBS5-5;Q9UBS5- 1 1 2,8 65,081 Gamma-aminobutyric acid type B 3;Q9UBS5-4;Q9UBS5 receptor subunit 1

DKK2 Q9UBU2 2 2 12,4 28,447 Dickkopf-related protein 2 SEL1L Q9UBV2-2;Q9UBV2 3 3 19,6 33,53 Protein sel-1 homolog 1 CTSF Q9UBX1 12 12 33,5 53,365 Cathepsin F FBLN5 Q9UBX5 8 8 25 50,18 Fibulin-5 KLK11 Q9UBX7- 7 7 46,8 27,465 Kallikrein-11;Kallikrein-11 inactive 1;Q9UBX7;Q9UBX7- chain 1;Kallikrein-11 inactive chain 2 4;Q9UBX7-3 PPP1R1B Q9UD71;Q9UD71-2 2 2 22,5 22,963 Protein phosphatase 1 regulatory subunit 1B

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] DNAJB4 Q9UDY4 1 1 3,9 37,806 DnaJ homolog subfamily B member 4 PLEKHB1 Q9UF11-4;Q9UF11- 2 2 9 21,254 Pleckstrin homology domain- 2;Q9UF11-3;Q9UF11 containing family B member 1

EPHA6 Q9UF33 6 6 7,6 116,38 Ephrin type-A receptor 6 FAM198A Q9UFP1 10 10 26,4 63,637 Protein FAM198A DMBT1 Q9UGM3-9;Q9UGM3- 1 1 2,5 124,45 Deleted in malignant brain tumors 1 4;Q9UGM3- protein 8;Q9UGM3- 2;Q9UGM3- 5;Q9UGM3- 3;Q9UGM3;Q9UGM3- 7;Q9UGM3-6

FETUB Q9UGM5;Q9UGM5-2 10 10 40,6 42,054 Fetuin-B

CD300A Q9UGN4 1 1 6 33,2 CMRF35-like molecule 8 SUSD2 Q9UGT4 2 2 4,1 90,207 Sushi domain-containing protein 2 SUN2 Q9UH99- 1 1 2,2 79,611 SUN domain-containing protein 2 3;Q9UH99;Q9UH99-2

LAMTOR3 Q9UHA4-2;Q9UHA4 1 1 8,5 12,941 Ragulator complex protein LAMTOR3

CNTNAP2 Q9UHC6 26 26 25,7 148,17 Contactin-associated protein-like 2 TAC3 Q9UHF0;Q9UHF0- 3 3 34,7 13,438 Tachykinin-3;Neurokinin-B 3;Q9UHF0-2 PCSK1N Q9UHG2 10 9 63,8 27,372 ProSAAS;KEP;Big SAAS;Little SAAS;Big PEN-LEN;PEN;Little LEN;Big LEN PCYOX1 Q9UHG3-2;Q9UHG3 8 8 21,5 48,506 Prenylcysteine oxidase 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] ADAMTS1 Q9UHI8 4 4 9,7 105,36 A disintegrin and metalloproteinase with thrombospondin motifs 1 DPP7 Q9UHL4 14 14 36,2 54,341 Dipeptidyl peptidase 2 ENOPH1 Q9UHY7;Q9UHY7-2 6 6 40,2 28,932 Enolase-phosphatase E1 TAGLN3 Q9UI15 5 5 30,7 22,472 Transgelin-3 CD84 Q9UIB8-6;Q9UIB8- 1 1 9,1 26,902 SLAM family member 5 5;Q9UIB8-4;Q9UIB8- 3;Q9UIB8-2;Q9UIB8

TMEFF2 Q9UIK5- 2 2 6,1 38,132 Tomoregulin-2 2;Q9UIK5;Q9UIK5-3

LNPEP Q9UIQ6-3;Q9UIQ6- 2 2 2,1 115,06 Leucyl-cystinyl aminopeptidase;Leucyl- 2;Q9UIQ6 cystinyl aminopeptidase, pregnancy serum form PLXNA1 Q9UIW2 5 5 4,2 211,06 Plexin-A1 CDH22 Q9UJ99 6 6 11,2 89,09 Cadherin-22 ENPP5 Q9UJA9 4 4 9 54,665 Ectonucleotide pyrophosphatase/phosphodiesterase family member 5 SH3BGRL2 Q9UJC5 1 1 11,2 12,326 SH3 domain-binding glutamic acid- rich-like protein 2 METRN Q9UJH8 2 2 11,3 31,207 Meteorin GNPTG Q9UJJ9 6 6 28,9 33,973 N-acetylglucosamine-1- phosphotransferase subunit gamma LAMP5 Q9UJQ1-2;Q9UJQ1 2 2 12,3 26,51 Lysosome-associated membrane glycoprotein 5 FBXO2 Q9UK22 3 3 10,8 33,327 F-box only protein 2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] NAGPA Q9UK23-3;Q9UK23- 2 2 8,1 33,576 N-acetylglucosamine-1- 2;Q9UK23 phosphodiester alpha-N- acetylglucosaminidase TMEM59L Q9UK28 7 7 32,5 37,619 Transmembrane protein 59-like SERPINA10 Q9UK55;CON__ENSEM 7 7 21,2 50,706 Protein Z-dependent protease BL:ENSBTAP000000130 inhibitor 50 HN1 Q9UK76-3;Q9UK76 1 1 38,9 11,023 Hematological and neurological expressed 1 protein;Hematological and neurological expressed 1 protein, N-terminally processed AKAP11 Q9UKA4 2 2 1,9 210,51 A-kinase anchor protein 11 AJAP1 Q9UKB5 3 3 11,7 44,536 Adherens junction-associated protein 1 NUDT5 Q9UKK9 3 3 18,7 24,327 ADP-sugar pyrophosphatase MAN1B1 Q9UKM7 10 10 17,9 79,579 Endoplasmic reticulum mannosyl- oligosaccharide 1,2-alpha- mannosidase ADAM28 Q9UKQ2-2;Q9UKQ2 4 4 5,7 61,232 Disintegrin and metalloproteinase domain-containing protein 28 TRHDE Q9UKU6 8 8 8,4 117 Thyrotropin-releasing hormone- degrading ectoenzyme ANGPTL2 Q9UKU9;Q9UKU9- 8 8 22,9 57,104 Angiopoietin-related protein 2 2;Q8NI99 PRND Q9UKY0 1 1 5,1 20,293 Prion-like protein doppel CDV3 Q9UKY7-2;Q9UKY7 2 2 10,8 22,079 Protein CDV3 homolog TENM1 Q9UKZ4;Q9UKZ4-2 5 5 3,6 305,01 Teneurin-1;Ten-1 intracellular domain;Teneurin C-terminal- associated peptide

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] NRXN1 Q9ULB1-2;Q9ULB1- 44 30 39,1 164,65 Neurexin-1 3;Q9ULB1;Q9ULB1-4

CDH9 Q9ULB4 8 7 13,9 88,688 Cadherin-9 CDH7 Q9ULB5 8 8 15,8 87,085 Cadherin-7 SLC39A10 Q9ULF5 7 7 12 94,131 Zinc transporter ZIP10 LRFN2 Q9ULH4 6 6 9,6 84,73 Leucine-rich repeat and fibronectin type-III domain-containing protein 2 HEG1 Q9ULI3;Q9ULI3-2 8 8 10,3 147,46 Protein HEG homolog 1 PLXNB3 Q9ULL4;Q9ULL4-2 12 12 9,9 206,84 Plexin-B3 NDRG4 Q9ULP0-7;Q9ULP0- 5 5 21,1 40,049 Protein NDRG4 4;Q9ULP0- 2;Q9ULP0;Q9ULP0- 8;Q9ULP0-5;Q9ULP0- 3;Q9ULP0-6

RNF112 Q9ULX5;Q9ULX5-2 1 1 2,1 68,297 RING finger protein 112 CA14 Q9ULX7 2 2 8,6 37,667 PYCARD Q9ULZ3-3;Q9ULZ3- 2 2 17,8 15,03 -associated speck-like 2;Q9ULZ3 protein containing a CARD MMP17 Q9ULZ9;Q9ULZ9-2 7 7 18,6 66,652 Matrix metalloproteinase-17 MGAT4A Q9UM21-2;Q9UM21 1 1 3,3 48,946 Alpha-1,3-mannosyl-glycoprotein 4- beta-N-acetylglucosaminyltransferase A;Alpha-1,3-mannosyl-glycoprotein 4- beta-N-acetylglucosaminyltransferase A soluble form EPDR1 Q9UM22;Q9UM22- 2 2 10,3 25,437 Mammalian ependymin-related 2;Q9UM22-3 protein 1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] NOTCH3 Q9UM47 16 16 12,5 243,63 Neurogenic locus notch homolog protein 3;Notch 3 extracellular truncation;Notch 3 intracellular domain ICAM5 Q9UMF0 19 19 32,8 97,115 Intercellular adhesion molecule 5 UBQLN1;UBQLN2 Q9UMX0-4;Q9UMX0- 2 2 16,6 18,909 Ubiquilin-1;Ubiquilin-2 2;Q9UMX0;Q9UHD9

NENF Q9UMX5 7 7 57,6 18,856 Neudesin NDRG2 Q9UN36-2;Q9UN36- 8 8 40,9 39,289 Protein NDRG2 6;Q9UN36;Q9UN36- 3;Q9UN36-4;Q9UN36-5

PCDHGC3 Q9UN70;Q9UN70-2 7 6 11,3 101,08 Protocadherin gamma-C3

PCDHA7;PCDHA4;PCDHA Q9UN72-2;Q9UN74- 2 1 4,4 84,895 Protocadherin alpha-7;Protocadherin 9 2;Q9Y5H5- alpha-4;Protocadherin alpha-9 2;Q9UN72;Q9UN74;Q9 Y5H5

PCDHA6;PCDHA8;PCDHA Q9UN73- 3 2 5,1 86,844 Protocadherin alpha-6;Protocadherin 5 3;Q9UN73;Q9UN73- alpha-8;Protocadherin alpha-5 2;Q9Y5H6-2;Q9Y5H7- 2;Q9Y5H7- 3;Q9Y5H7;Q9Y5H6;Q9Y 5I0-2;Q9Y5H8- 2;Q9Y5I0;Q9Y5H8

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PROCR Q9UNN8 4 4 18,9 26,671 Endothelial protein C receptor MINPP1 Q9UNW1;Q9UNW1- 13 13 36,6 55,051 Multiple inositol polyphosphate 4;Q9UNW1- phosphatase 1 3;Q9UNW1-2 NSFL1C Q9UNZ2- 1 1 6,2 28,522 NSFL1 cofactor p47 6;Q9UNZ2;Q9UNZ2-5

ADAMTS8 Q9UP79 9 9 19,2 96,459 A disintegrin and metalloproteinase with thrombospondin motifs 8 BSN Q9UPA5 2 2 1,1 416,46 Protein bassoon SLC8A2 Q9UPR5 2 2 4,2 100,37 Sodium/calcium exchanger 2 SORCS3 Q9UPU3 15 14 17,5 135,75 VPS10 domain-containing receptor SorCS3 THSD7A Q9UPZ6 4 4 3,4 185,36 Thrombospondin type-1 domain- containing protein 7A CNTN6 Q9UQ52 27 26 39,6 113,95 Contactin-6 MGAT4B Q9UQ53- 4 4 10,8 63,069 Alpha-1,3-mannosyl-glycoprotein 4- 2;Q9UQ53;Q9UQ53-3 beta-N-acetylglucosaminyltransferase B CAMK2A Q9UQM7;Q9UQM7-2 5 4 15,9 54,087 Calcium/calmodulin-dependent protein kinase type II subunit alpha TNN Q9UQP3 2 2 2,3 144,03 Tenascin-N JAG2 Q9Y219-2;Q9Y219 3 3 4,5 129,23 Protein jagged-2 ENTPD4 Q9Y227-2;Q9Y227 2 2 3,8 69,42 Ectonucleoside triphosphate diphosphohydrolase 4 CLEC11A Q9Y240 7 7 24,5 35,694 C-type lectin domain family 11 member A NUDC Q9Y266 4 4 13 38,242 Nuclear migration protein nudC ST3GAL6 Q9Y274;Q9Y274-2 5 5 16 38,213 Type 2 lactosamine alpha-2,3- sialyltransferase

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] TNFSF13B Q9Y275;Q9Y275- 3 3 19,3 31,222 Tumor necrosis factor ligand 2;Q9Y275-3 superfamily member 13B;Tumor necrosis factor ligand superfamily member 13b, membrane form;Tumor necrosis factor ligand superfamily member 13b, soluble form VSIG4 Q9Y279- 6 6 32,1 35,543 V-set and immunoglobulin domain- 2;Q9Y279;Q9Y279-3 containing protein 4

CFL2 Q9Y281-3;Q9Y281 4 1 32,2 16,916 Cofilin-2 ITM2B Q9Y287;Q9Y287-2 11 11 61,3 30,338 Integral membrane protein 2B;BRI2, membrane form;BRI2 intracellular domain;BRI2C, soluble form;Bri23 peptide CNPY2 Q9Y2B0;Q9Y2B0-2 4 4 31,3 20,652 Protein canopy homolog 2 MAN2B2 Q9Y2E5;Q9Y2E5-2 8 8 11 113,98 Epididymis-specific alpha-mannosidase MYRF Q9Y2G1-2;Q9Y2G1 4 4 6 120,22 Myelin regulatory factor;Myelin regulatory factor, N-terminal;Myelin regulatory factor, C-terminal STK38L Q9Y2H1 1 1 3,2 54,002 Serine/threonine-protein kinase 38- like NTNG1 Q9Y2I2-1;Q9Y2I2- 10 10 29,5 49,34 Netrin-G1 5;Q9Y2I2-4;Q9Y2I2- 6;Q9Y2I2;Q9Y2I2-2 RPH3A Q9Y2J0-2;Q9Y2J0 2 2 6,4 76,385 Rabphilin-3A EPB41L3 Q9Y2J2-2;Q9Y2J2- 4 4 7,6 96,513 Band 4.1-like protein 3;Band 4.1-like 4;Q9Y2J2 protein 3, N-terminally processed GDA Q9Y2T3;Q9Y2T3- 20 20 55,9 51,002 Guanine deaminase 3;Q9Y2T3-2

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] MEMO1 Q9Y316- 1 1 6,2 31,307 Protein MEMO1 2;Q9Y316;Q9Y316-3

VWA7 Q9Y334-2;Q9Y334 4 4 8,5 92,512 von Willebrand factor A domain- containing protein 7 SIGLEC9 Q9Y336;Q9Y336-2 1 1 3,2 50,081 Sialic acid-binding Ig-like lectin 9 RNF11 Q9Y3C5 1 1 7,8 17,444 RING finger protein 11 TLN1 Q9Y490 4 3 2,2 269,76 -1 NRXN3 Q9Y4C0;Q9Y4C0-3 39 1 29,9 180,6 Neurexin-3 NRXN3 Q9Y4C0-4 40 2 35,8 153,88 Neurexin-3 PLXND1 Q9Y4D7-2;Q9Y4D7 5 5 3 195,56 Plexin-D1 HYOU1 Q9Y4L1;Q9Y4L1- 25 25 31,8 111,33 Hypoxia up-regulated protein 1 2;Q9BXT5 PPME1 Q9Y570- 1 1 11,1 22,461 Protein phosphatase methylesterase 1 2;Q9Y570;Q9Y570-4

PCDHB9;PCDHB10 Q9Y5E1;Q9UN67 3 3 4,8 87,098 Protocadherin beta-9;Protocadherin beta-10 PCDHB4 Q9Y5E5 1 1 1,5 87,269 Protocadherin beta-4 PCDHB15 Q9Y5E8 2 2 3,9 86,328 Protocadherin beta-15 PCDHGC5 Q9Y5F6;Q9Y5F6-2 14 13 28,2 101,92 Protocadherin gamma-C5 PCDHGC4 Q9Y5F7;Q9Y5F7-2 7 6 12,2 101,21 Protocadherin gamma-C4 PCDHGB7 Q9Y5F8;Q9Y5F8-2 3 1 5,3 100,97 Protocadherin gamma-B7 PCDHGB5 Q9Y5G0;Q9Y5G0- 6 5 11,4 99,874 Protocadherin gamma-B5 2;Q9UN71;Q9Y5G3;Q9 Y5G2;Q9UN71- 2;Q9Y5G3-2;Q9Y5G2-2

PCDHGA6 Q9Y5G7;Q9Y5G7-2 5 2 6,5 100,87 Protocadherin gamma-A6

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] PCDHGA3 Q9Y5H0;Q9Y5H0-2 4 1 5,9 100,97 Protocadherin gamma-A3 PCDHGA2 Q9Y5H1;Q9Y5H1-2 4 1 5,6 101,48 Protocadherin gamma-A2 PCDHGA10 Q9Y5H3;Q9Y5H3-2 5 1 6,7 101,45 Protocadherin gamma-A10 PCDHA10;PCDHA11 Q9Y5I2-2;Q9Y5I1- 1 1 2,2 75,741 Protocadherin alpha-10;Protocadherin 2;Q9Y5I2- alpha-11 3;Q9Y5I2;Q9Y5I1 PCDHAC2 Q9Y5I4- 13 13 17 96,195 Protocadherin alpha-C2 2;Q9Y5I4;O75153 MMP24 Q9Y5R2 2 2 4 73,231 Matrix metalloproteinase- 24;Processed matrix metalloproteinase-24 WIF1 Q9Y5W5 2 2 8,2 41,527 Wnt inhibitory factor 1 LIPG Q9Y5X9 2 2 3,6 56,794 LYVE1 Q9Y5Y7 8 8 24,2 35,213 Lymphatic vessel endothelial receptor 1 HEBP2 Q9Y5Z4;Q9Y5Z4-2 3 3 19,5 22,875 Heme-binding protein 2 PSAT1 Q9Y617;Q9Y617-2 10 10 32,7 40,422 Phosphoserine aminotransferase NPTN Q9Y639-4;Q9Y639- 4 4 14,5 37,791 Neuroplastin 5;Q9Y639;Q9Y639- 3;Q9Y639-1 RFNG Q9Y644 1 1 5,4 36,423 Beta-1,3-N- acetylglucosaminyltransferase radical fringe CPQ Q9Y646 13 13 36,9 51,887 Carboxypeptidase Q GPR56 Q9Y653-5;Q9Y653- 4 4 10,4 58,041 G-protein coupled receptor 56;GPR56 2;Q9Y653- N-terminal fragment;GPR56 C-terminal 3;Q9Y653;Q9Y653-4 fragment

CLIC4 Q9Y696 7 7 48,6 28,772 Chloride intracellular channel protein 4 EMILIN1 Q9Y6C2 4 4 5 106,67 EMILIN-1

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476 Supplementary material J Neurol Neurosurg Psychiatry

Gene names Protein IDs Peptides Unique Sequence Mol. weight Protein names peptides coverage [%] [kDa] WNT6 Q9Y6F9 1 1 4,9 39,72 Protein Wnt-6 LAMC3 Q9Y6N6 6 6 5,4 171,23 Laminin subunit gamma-3 ROBO1 Q9Y6N7- 25 23 22,6 176,57 Roundabout homolog 1 4;Q9Y6N7;Q9Y6N7- 2;Q9Y6N7-6;Q9Y6N7- 5;Q9Y6N7-3

CDH10 Q9Y6N8 8 7 13,3 88,45 Cadherin-10 TNFRSF11A Q9Y6Q6;Q9Y6Q6- 2 2 9,9 66,033 Tumor necrosis factor receptor 4;Q9Y6Q6-2;Q9Y6Q6- superfamily member 11A 3;Q9Y6Q6-5;Q9Y6Q6-6

FCGBP Q9Y6R7 76 76 34,4 572,01 IgGFc-binding protein ENPP4 Q9Y6X5;Q6UWV6 6 6 19,2 51,641 Bis(5-adenosyl)-triphosphatase ENPP4

Barschke P, et al. J Neurol Neurosurg Psychiatry 2020;0:1–9. doi: 10.1136/jnnp-2019-322476