Supplementary material J Neurol Neurosurg Psychiatry Gene names Protein IDs Peptides 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 growth factor-like 2;A6BM72;A6BM72- domains protein 11 4;A6BM72-3 PGP A6NDG6 1 1 5,9 34,006 Phosphoglycolate phosphatase 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 Olfactory receptor 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 Proline-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 Deoxyribonuclease-2-alpha ACOT7 O00154-6;O00154- 1 1 4,9 36,567 Cytosolic acyl coenzyme A thioester 4;O00154-5;O00154- hydrolase 7;O00154 MASP2 O00187;O00187-2 3 3 6,6 75,702 Mannan-binding lectin serine protease 2;Mannan-binding lectin serine protease 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 membrane protein 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;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 cell adhesion molecule L1-like protein;Processed neural cell adhesion molecule 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 Ribonuclease 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 peptide;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 tyrosine-protein phosphatase T ASTN1 O14525- 6 6 7,5 143,98 Astrotactin-1 2;O14525;O14525-3 NCAN O14594 23 22 23,5 143,09 Neurocan 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 Disintegrin and metalloproteinase domain-containing protein 10 SLC9A3R1 O14745;O14745-2 2 2 6,4 38,868 Na(+)/H(+) exchange regulatory cofactor NHE-RF1 TPP1 O14773;O14773-2 11 11 29 61,247 Tripeptidyl-peptidase 1 NRP1 O14786-3;O14786- 14 14 38,1 68,375 Neuropilin-1 2;O14786 APOL1 O14791- 8 8 19,2 42,158 Apolipoprotein 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 Protocadherin-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 thrombospondin motifs 3 DCLK1 O15075-2;O15075 1 1 1,5 81,099 Serine/threonine-protein kinase 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 Actin-related protein 2/3 complex subunit 1B EPHB6 O15197- 8 8 29,6 57,497 Ephrin 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 Laminin 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 Syntaxin-7 ST8SIA5 O15466;O15466-2 4 4 14,4 43,894 Alpha-2,8-sialyltransferase 8E FABP7 O15540;O15540-2 2 2 25 14,889 Fatty acid-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 dynein 1 light intermediate chain 2 KLK10 O43240 2 2 10,1 30,17 Kallikrein-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 Glutamate receptor 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.