Supporting Information for Proteomics DOI 10.1002/pmic.200700455

Yuko Ogata, M. Cristine Charlesworth, LeeAnn Higgins, B. Mark Keegan, Steven Vernino and David C. Muddiman

Differential expression in male and female human lumbar cerebrospinal fluid using iTRAQ reagents after abundant protein depletion

ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Appendix A

Protein/protein groups identified (95% confidence level).

Total Number Accession Protein Name ProtScore 1 gi|40786791 complement component 3 70 gi|4557385 complement component 3 precursor 2 gi|57209519 complement component C4B 61.4 gi|2347136 complement component C4 3 gi|4557225 alpha-2-macroglobulin precursor 44.14 gi|62088808 Alpha 2 macroglobulin variant gi|51476396 hypothetical protein gi|46812315 alpha 2 macroglobulin 4 gi|455970 vitamin D-binding protein/group specific component 33.22 gi|181482 serum vitamin D-binding protein precursor Chain A, Crystal Structure Of The Complex Of Human Vitamin D Binding Protein And gi|28373620 Rabbit Muscle 5 gi|37182631 DPKL1915 29.05 6 gi|15217079 pigment epithelium-derived factor 28 7 gi|6013427 serum albumin precursor 27.39 Chain A, Human Serum Albumin Mutant R218p Complexed With Thyroxine (3,3',5,5'- gi|31615331 Tetraiodo-L-Thyronine) gi|52001697 serum albumin precursor Chain A, Human Serum Albumin Complexed With Myristic Acid And The S- (-) gi|14719645 Enantiomer Of Warfarin gi|51476390 hypothetical protein 8 gi|22137786 ENPP2 protein 25.1 gi|1160616 autotaxin-t 9 gi|4557485 ceruloplasmin (ferroxidase) 25.05

gi|1942284 X-Ray Crystal Structure Of Human Ceruloplasmin At 3.0 Angstroms

10 gi|56203410 complement factor H 23.49 Chain A, Four Models Of Human Factor H Determined By Solution Scattering Curve- gi|40890037 Fitting And Homology 11 gi|338057 sulfated -2 22.62 gi|42740907 isoform 2 gi|178855 J precursor gi|42716297 clusterin isoform 1 gi|180620 complement cytolysis inhibitor precursor 12 gi|38044288 gelsolin isoform b 21.52 13 gi|178775 proapolipoprotein 21.1 gi|178777 proapo-A-I protein gi|37499465 apolipoprotein A-I 14 gi|62089004 chromogranin B precursor variant 21.1 angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 15 gi|30582541 20 antiproteinase, antitry gi|532198 angiotensinogen gi|62089124 angiotensinogen precursor variant angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 gi|55959990 antiproteinase, antitry

angiotensinogen (serine (or cysteine) proteinase inhibitor, clade A (alpha-1 gi|37790798 antiproteinase, antitry 16 gi|2146954 hevin precursor - human 19.4 gi|21707436 SPARC-like 1 gi|21359871 SPARC-like 1 17 gi|178849 19.1 gi|178851 preapolipoprotein E 18 gi|62088238 Neural cell adhesion molecule variant 19.1 gi|2190958 neural cell adhesion molecule gi|27894376 cell adhesion molecule with homology to L1CAM precursor 19 gi|178779 apolipoprotein A-IV precursor 18.57 20 gi|1335098 unnamed protein product 18 gi|11321561 gi|386789 hemopexin precursor 21 gi|4885065 amyloid beta (A4) precursor-like protein 1 18 gi|1709301 amyloid precursor-like protein 1

22 gi|48425163 Chain I, Crystal Structure Of P13 Alanine Variant Of Antithrombin 18

gi|8569385 Chain I, N135q-S380c-Antithrombin-Iii gi|179161 antithrombin III Chain I, 2.5a Crystal Structure Of The Antithrombin--Heparin Ternary gi|52695711 Complex gi|8569387 Chain I, P14-Fluorescein-N135q-S380c-Antithrombin-Iii 23 gi|1335344 unnamed protein product 17.05 gi|4503635 factor II precursor gi|30802115 Coagulation factor II, precursor 24 gi|37183303 secretogranin 16.82 gi|15778922 Secretogranin III 25 gi|414791 contactin 16.62 gi|28373117 contactin 1 isoform 1 precursor gi|28373119 contactin 1 isoform 2 precursor 26 gi|3983127 monocyte antigen CD14 precursor 16 gi|30583501 CD14 antigen 27 gi|8918224 Dickkopf-3 15.52 28 gi|57209501 B-factor, properdin 14.25 gi|14124934 Complement factor B, preproprotein gi|2347133 complement factor B

29 gi|6832905 Chromogranin A precursor (CgA) (Pituitary secretory protein I) (SP-I) 14

gi|30582577 chromogranin A (parathyroid secretory protein 1) gi|40225646 CHGA protein gi|2072129 chromogranin A 30 gi|16924233 SPP1 protein 14 gi|22761565 unnamed protein product 31 gi|36573 unnamed protein product 14 gi|18201911 precursor gi|139653 Vitronectin precursor (Serum spreading factor) (S-protein) (V75) 32 gi|899271 complement C7 13.52

2 gi|45580688 complement component 7 precursor 33 gi|30582543 kallikrein 6 (neurosin, zyme) 13.05

gi|21465525 Chain A, Human Prokallikrein 6 (Hk6) PROZYME PROPROTEASE M Proneurosin

Chain A, Human Kallikrein 6 (Hk6) Active Form With Benzamidine Inhibitor At 1.56 A gi|21466131 Resolution 34 gi|31419 fibulin-1 C 12.32 gi|18490682 Fibulin 1, isoform C precursor gi|34734062 fibulin 1 isoform C precursor 35 gi|1197209 alpha-1-acid glycoprotein 1 precursor 12 gi|54696442 1 36 gi|609449 amyloid precursor protein 12 gi|41350939 Amyloid beta A4 protein, precursor, isoform b gi|178616 amyloid-beta protein gi|178615 amyloid-beta protein 37 gi|33356541 transfer protein isoform b precursor 12 gi|18044721 Phospholipid transfer protein, isoform a precursor gi|3191967 GD:PLTP

38 gi|54300696 serine/cysteine proteinase inhibitor clade G member 1 splice variant 2 12

gi|1340170 unnamed protein product gi|179619 plasma protease (C1) inhibitor precursor gi|20385946 C1 esterase inhibitor gi|62089238 Plasma protease C1 inhibitor precursor variant 39 gi|33315782 non-classical cadherin XB31alpha1 12 gi|54125663 alcadein alpha-1 gi|21706696 Calsyntenin 1, isoform 2 40 gi|34365170 hypothetical protein 11.52 gi|16933542 fibronectin 1 isoform 3 preproprotein gi|47132549 fibronectin 1 isoform 6 preproprotein gi|47132557 fibronectin 1 isoform 1 preproprotein gi|53791223 fibronectin 1 41 gi|1439613 neural cell adhesion molecule CD56; N-CAM 11.52 gi|10834990 neural cell adhesion molecule 1 gi|35006 unnamed protein product gi|62088466 Neural cell adhesion molecule 1, 120 kDa isoform precursor variant gi|41281937 neural cell adhesion molecule 1 42 gi|4165890 alpha-1-antichymotrypsin precursor 11.52 gi|1340142 alpha1-antichymotrypsin gi|225769 chymotrypsin inhibitor

gi|50659080 serine (or cysteine) proteinase inhibitor, clade A, member 3 precursor

Chain A, Alpha1-Antichymotrypsin Serpin In The Delta Conformation (Partial Loop gi|6980544 Insertion) 43 gi|619383 , apoD 11.1 44 gi|5802984 beta-1,3-N-acetylglucosaminyltransferase bGnT-6 11.1 45 gi|30583217 transthyretin (prealbumin, amyloidosis type I) 11.05 Chain B, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And gi|2098256 Implications For Amyl

3 Chain B, Tertiary Structures Of Three Amyloidogenic Transthyretin Variants And gi|3891561 Implications For Amyl

Chain D, The Monoclinic Crystal Struture Of Transthyretin In Complex With gi|56554067 Diethylstilbestrol gi|339685 transthyretin

46 gi|6651381 NgCAM-related related cell adhesion molecule /alternative carboxyl terminus 10.05

gi|40788219 KIAA0343 Neuronal cell adhesion molecule precursor (Nr-CAM) (NgCAM-related cell adhesion gi|33112413 molecule) (Ng-CAM-re gi|1621283 hBRAVO/Nr-CAM precursor gi|6651380 NgCAM-related related cell adhesion molecule 47 gi|48145977 ORM2 12 gi|29170378 alpha-1-acid glycoprotein 2 precursor gi|55958975 orosomucoid 2 48 gi|30582517 cystatin C (amyloid angiopathy and cerebral hemorrhage) 10

gi|14278690 Chain A, Human Cystatin C; Dimeric Form With 3d Domain Swapping

gi|181387 cystatin C 49 gi|48145609 PSAP 9.52

gi|57209714 prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy)

gi|220064 sphingolipid activator

gi|30582537 prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy)

gi|62089138 prosaposin variant 50 gi|55960460 contactin 2 (axonal) 9.4 gi|444868 TAG-1 protein (axonin 1)

51 gi|123055 Heparin cofactor II precursor (HC-II) (Protease inhibitor leuserpin 2) (HLS2) 9.11

gi|47678677 SERPIND1

gi|23200176 Chain A, Crystal Structure Of The Heparin Cofactor Ii-S195a Thrombin Complex

gi|1335104 unnamed protein product gi|23273330 Heparin cofactor II 52 gi|69990 alpha-1-B-glycoprotein - human 9.1 gi|46577680 Alpha-1B-glycoprotein precursor (Alpha-1-B glycoprotein)

53 gi|9665253 EGF-containing fibulin-like extracellular matrix protein 1 isoform b 9.1

gi|15072400 EGF-containing fibulin-like extracellular matrix protein 1 54 gi|30582659 cathepsin D (lysosomal aspartyl protease) 8.19 55 gi|4557327 apolipoprotein H precursor 8

gi|6573461 Chain A, Crystal Structure Of Human Beta-2-Glycoprotein-I (Apolipoprotein-H)

Chain A, Crystal Structure Of The Glycosylated Five-Domain Human Beta2- gi|6435718 Glycoprotein I Purified From gi|32165624 apolipoprotein H (beta-2-glycoprotein I) 56 gi|30582147 insulin-like growth factor binding protein 7 8 57 gi|1360676 collagen alpha 1(VI) chain precursor - human 8 gi|30851190 Collagen, type VI, alpha 1, precursor

4 gi|13878903 Collagen alpha 1(VI) chain precursor gi|15011913 collagen, type VI, alpha 1 precursor 58 gi|47479594 Histidine-rich glycoprotein, precursor 8 59 gi|56203917 plasminogen 8 gi|38051823 Plasminogen gi|190026 plasminogen gi|387026 plasminogen 60 gi|34785163 Complement component 1, s subcomponent 8 61 gi|4501987 afamin precursor 8 62 gi|12804001 Proprotein convertase subtilisin/kexin type 1 inhibitor, precursor 8 63 gi|31853 G(M2) activator protein 8 gi|673416 GM2 activator protein gi|14424507 GM2 activator, precursor gi|226416 Gm2 activator protein gi|14278641 Chain C, Human Gm2 Activator Structure 64 gi|55962673 prostaglandin D2 synthase 21kDa (brain) 7.52 gi|55962672 prostaglandin D2 synthase 21kDa (brain) 65 gi|29387000 Alpha-2-HS-glycoprotein 7.52 gi|2521981 alpha2-HS glycoprotein gi|2521983 alpha2-HS glycoprotein 66 gi|5817233 hypothetical protein 7.4 gi|33150528 OG 67 gi|30582253 7.22 gi|642534 lumican 68 gi|17402890 neuronal pentraxin receptor isoform 2 6.62 gi|57208136 OTTHUMP00000028666 gi|17402888 neuronal pentraxin receptor isoform 1 69 gi|4502147 amyloid beta (A4) precursor-like protein 2 6.57 gi|291856 amyloid protein gi|12653211 APLP2 protein gi|5702388 amyloid precursor protein homolog HSD-2 70 gi|21619841 PTPNS1 protein 6 gi|56203949 PTPNS1 71 gi|483474 90K 6 72 gi|125507 Kininogen precursor (Alpha-2-thiol proteinase inhibitor) 6 gi|386852 kininogen 73 gi|55957384 OTTHUMP00000063975 6 74 gi|3660227 Human -I, Nmr, 18 Structures 6 75 gi|51476755 hypothetical protein 5.52 76 gi|37674422 unknown 5.4 77 gi|37499463 apolipoprotein C-III 5.1 gi|224917 CIII gi|521205 apolipoprotein C-III 78 gi|31565487 Carboxypeptidase E, precursor 5.1 gi|6429043 carboxypeptidase E Human Tetranectin, A Trimeric Plasminogen Binding Protein With An Alpha-Helical 79 gi|2781225 5.1 Coiled Coil 80 gi|54112390 calcium channel, voltage-dependent, alpha 2/delta subunit 1 5.1

gi|1705852 Dihydropyridine-sensitive L-type, calcium channel alpha-2/delta subunits precursor

5 gi|6090615 dihydropyridine receptor alpha 2 subunit 81 gi|55770878 neuronal pentraxin I precursor 5.1 gi|2499457 Neuronal pentraxin-1 precursor (NP1) (Neuronal pentraxin I) (NP-I) 82 gi|55743122 retinol-binding protein 4, plasma precursor 5.1 Chain F, The Structure Of Human Retinol Binding Protein With Its Carrier Protein gi|4558180 Transthyretin Revea gi|230284 Retinol Binding Protein gi|35897 unnamed protein product gi|18088326 Retinol-binding protein 4, plasma, precursor 83 gi|339683 Thy-1 5.1 gi|62087998 Thy-1 cell surface antigen variant gi|41350921 Thy-1 cell surface antigen 84 gi|21594846 Alpha-2-plasmin inhibitor 5.05 gi|11386143 alpha-2-plasmin inhibitor

gi|112907 Alpha-2-antiplasmin precursor (Alpha-2-plasmin inhibitor) (Alpha-2-PI) (Alpha-2-AP)

85 gi|55958792 cartilage acidic protein 1 5.05 gi|10178883 chondrocyte expressed protein 68 kDa gi|19171211 CRTAC1-B protein gi|9368808 ASPIC 86 gi|4503681 Fc fragment of IgG binding protein 4.52 gi|5080756 Human Fc gamma BP [AA 1-2843] [Homo sapiens] 87 gi|38489880 superoxide dismutase 4 gi|34809797 Chain J, Structure Of Human Cu,Zn Superoxide Dismutase Chain C, Crystal Structure Of Fals-Associated Human Copper-Zinc Superoxide gi|34810330 Dismutase (Cuznsod) Mutan

Chain A, Solution Structure Of Apo Cu,Zn Superoxide Dismutase: Role Of Metal Ions gi|39654883 In Protein Folding gi|1237406 Cu/Zn-superoxide dismutase 88 gi|45594240 limbic system-associated membrane protein 4 gi|2497323 Limbic system-associated membrane protein precursor (LSAMP) 89 gi|56204820 GD:RP11-514O12.3 4 gi|20145505 extra-cellular ribonuclease gi|7435275 ribonuclease 6 (EC 3.1.27.-) precursor - human gi|20145501 extra-cellular ribonuclease gi|20145503 extra-cellular ribonuclease 90 gi|46397857 Nucleobindin 1 precursor (CALNUC) 4 gi|32879999 nucleobindin 1 gi|1144316 nucleobindin gi|189308 nucleobindin 91 gi|50960747 Opioid-binding cell adhesion molecule, precursor 4 92 gi|4139514 Chain B, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair 4 gi|2624794 Chain B, Bm-40, FsEC DOMAIN PAIR 93 gi|55249559 DF protein 4 gi|15131535 adipsin/complement factor D precursor Complement factor D precursor (C3 convertase activator) (Properdin factor D) gi|3915626 (Adipsin) gi|5822045 Chain A, Structure Of 3,4-Dichloroisocoumarin-Inhibited Factor D gi|178626 adipsin/complement factor D 94 gi|253483 N-cadherin 4

6 gi|14589889 cadherin 2, type 1 preproprotein gi|319924 cadherin 2 precursor - human gi|22209070 Cadherin 2, type 1, preproprotein gi|1705541 Neural-cadherin precursor (N-cadherin) (Cadherin-2) 95 gi|62204502 Unknown (protein for MGC:111134) 4 gi|13529158 Secretory granule, neuroendocrine protein 1 (7B2 protein) Neuroendocrine protein 7B2 precursor (Secretory granule endocrine protein I) gi|23830842 (Secretogranin V) (Pitu gi|1585794 7B2 protein

96 gi|31542984 inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein) 4

gi|1483187 inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP)

Inter-alpha-trypsin inhibitor heavy chain H4 precursor (ITI heavy chain H4) (Inter- gi|13432192 alpha-inhibitor h

gi|62088356 inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein) variant

gi|4096840 inter-alpha-trypsin inhibitor family heavy chain-related protein 97 gi|51095101 protein tyrosine phosphatase, receptor-type, Z polypeptide 1 4

gi|300182 receptor-type protein tyrosine phosphatase beta, RPTP beta, PTP zeta

gi|3282241 tyrosine phosphatase zeta polypeptide 2 HTPZP2 Chain A, C-Terminal Domain Of Insulin-Like Growth Factor (Igf) Binding Protein-6: 98 gi|55669661 4 Structure And Inte gi|37953293 insulin-like growth factor binding protein 6 gi|183894 insulin-like growth factor binding protein 6 99 gi|4506801 secretogranin II precursor 4 100 gi|33010 unnamed protein product 4 gi|36968238 insulin-like growth factor binding protein 2, 36kDa gi|62088598 insulin-like growth factor binding protein 2 variant 101 gi|38614429 Diazepam binding inhibitor 4 Acyl-CoA-binding protein (ACBP) (Diazepam binding inhibitor) (DBI) (Endozepine) gi|118276 (EP) 102 gi|44917133 follistatin-related protein 4 103 gi|13874433 cerebral protein-12 4 gi|18088495 NELL2 protein 104 gi|54781351 superoxide dismutase 3, extracellular 4 105 gi|34616 beta-2 microglobulin 3.52

gi|4699634 Chain B, Mhc Class I H-2db Complexed With A Sendai Virus Nucleoprotein Peptide

pI 5.3 beta 2-microglobulin, BM [human, urine, chronic renal failure patient, Peptide, gi|1195503 98 aa]

Chain B, Crystal Structure Of Hla-B2705 Complexed With The Latent Membrane gi|56966290 Protein 2 Peptide (Lmp2)o

gi|34809953 Chain B, Crystal Structure Of Hla B4402 In Complex With Hla Dpa0201 Peptide

106 gi|62198241 6 open reading frame 82 isoform 1 3.52 gi|62526026 chromosome 6 open reading frame 82 isoform 3 gi|7341255 brain acetylcholinesterase putative membrane anchor

7 gi|56554583 Chain F, Divalent Cation Tolerant Protein Cuta From Homo Sapiens O60888

gi|62526024 chromosome 6 open reading frame 82 isoform 2 107 gi|4557032 lactate B 3.52 Chain D, Human B Lactate Dehydrogenase Complexed With Nad+ And 4- Hydroxy- gi|49259212 1,2,5-Oxadiazole-3-Carboxy

Chain B, Human Heart L-Lactate Dehydrogenase H Chain, Ternary Complex With gi|13786848 Nadh And Oxamate 108 gi|913159 neuropolypeptide h3 3.52 gi|4505621 prostatic binding protein gi|4261934 neuropolypeptide h3 109 gi|57284191 ATPase, H+ transporting, lysosomal accessory protein 1 3.52 gi|57284192 ATPase, H+ transporting, lysosomal accessory protein 1

gi|17136148 ATPase, H+ transporting, lysosomal accessory protein 1 precursor

gi|22761272 unnamed protein product gi|12053207 hypothetical protein 110 gi|34782802 PKM2 protein 3.1 gi|2117873 pyruvate kinase (EC 2.7.1.40), muscle splice form M1 - human gi|338827 cytosolic thyroid hormone-binding protein (EC 2.7.1.40) gi|33875497 Unknown (protein for IMAGE:2964687) gi|33286422 pyruvate kinase 3 isoform 2 111 gi|4504579 I factor (complement) 3.1 gi|1335056 unnamed protein product gi|1335054 unnamed protein product gi|116133 Complement factor I precursor (C3B/C4B inactivator) gi|224798 complement factor I light chain 112 gi|37674390 unknown 3.1 gi|386984 neuropeptide Y 113 gi|37182860 ISLR 3.05 114 gi|30583285 chitinase 3-like 1 (cartilage glycoprotein-39) 3.05 Chain D, Ligand-Induced Signalling And Conformational Change Of The 39 Kd gi|29726268 Glycoprotein From Human Ar gi|25058041 Chitinase 3-like 1 gi|4557018 chitinase 3-like 1 115 gi|39645299 VGF nerve growth factor inducible, precursor 3.05 116 gi|55961815 complement component 2 3.05 gi|34628 unnamed protein product gi|15277207 C2 gi|33346923 complement component 2 117 gi|37181420 AQGV3103 3.05 gi|16550719 unnamed protein product gi|15705411 recognition protein L precursor Chain E, Crystal Structure Of Fragment D Of Gammae132a Fibrinogen With The 118 gi|47168764 2.57 Peptide Ligand Gly-His-Ar gi|7924018 fibrinogen beta chain

gi|49258705 Chain E, Crystal Structure Of Fragment D Of Bbetad398a Fibrinogen

gi|28373962 Chain E, Fragment Double-D From Human Fibrin gi|223002 fibrin beta

8 119 gi|57209934 complement component 4A 59.4 gi|179674 complement component C4A serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment 120 gi|30583283 28 epithelium derived

121 gi|4389275 Human Serum Albumin In A Complex With Myristic Acid And Tri-Iodobenzoic Acid 27.39

122 gi|4502807 chromogranin B precursor 21.1 gi|5834566 GD:CHGB 123 gi|11281120 REIC protein - human 14 gi|37181881 DKK3 124 gi|15826034 Chain A, Apolipoprotein E3 22kd Fragment Lys146gln Mutant 12

gi|6980530 Chain A, Apolipoprotein E3 (Apoe3), Trigonal Truncation Mutant 165

gi|15826264 Chain A, Apolipoprotein E3 22kd Fragment Lys146glu Mutant gi|1942472 Apolipoprotein E2 (Apoe2, D154a Mutation) gi|1942471 Apolipoprotein E3 (Apoe3) 125 gi|443345 Chain A, Alpha1 Antichymotrypsin 11.52 126 gi|51476334 hypothetical protein 6 127 gi|1335074 unnamed protein product 4 128 gi|261745 beta-trace=23.5 kda glycoprotein {N-terminal} 2 gi|410564 beta-trace {N-terminal} 129 gi|38197157 UBC protein 2 gi|38114661 UBC protein gi|56967063 Chain D, Crystal Structure Of Uchl3-Ubvme Complex gi|15928840 UBC protein gi|51473011 PREDICTED: similar to Zgc:66168 protein 129 gi|56078799 Ubiquitin and ribosomal protein S27a, precursor 2 130 gi|62421176 actin-like protein 2 gi|62421136 actin-like protein gi|62421178 actin-like protein gi|62421148 actin-like protein gi|62421021 actin-like protein 131 gi|62088776 transforming growth factor, beta-induced, 68kDa variant 2 gi|2996636 BIGH3 gi|32879983 transforming growth factor, beta-induced, 68kDa 132 gi|37182089 SARG904 2 gi|21707216 MGC45438 protein gi|31543193 hypothetical protein LOC146556 133 gi|38196966 CD99L2 protein 2 gi|13899305 CD99 antigen-like 2 gi|20988862 CD99L2 protein 134 gi|7341430 NRXN3 2 gi|21070969 neurexin 3 isoform alpha precursor gi|17369927 Neurexin 3-alpha precursor (Neurexin III-alpha) gi|9454511 NRXNIII gi|40788347 KIAA0743 protein 135 gi|55959670 2 gi|18605564 Brevican, isoform 1 gi|37181869 Brevican Core Pro gi|55959671 brevican

9 gi|62088720 brevican isoform 1 variant 136 gi|4557373 biotinidase precursor 2 gi|1168695 Biotinidase precursor Serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), 137 gi|15929076 2 member 4 gi|1708609 Kallistatin precursor (Kallikrein inhibitor) (Protease inhibitor 4) gi|28375497 unnamed protein product 138 gi|30962903 Endoglycan 2 gi|37183309 podocalyxin-like protein 139 gi|38566166 Microfibrillar-associated protein 4 2 gi|23111005 microfibrillar-associated protein 4 gi|790817 microfibril-associated glycoprotein 4 140 gi|1335064 fibrillin 2 141 gi|2507615 neural cell adhesion protein 2 gi|33519481 neural cell adhesion molecule 2 precursor 142 gi|4502029 activated leukocyte cell adhesion molecule 2 gi|3183975 MEMD protein 143 gi|55959000 extracellular matrix protein 1 2 gi|4758236 extracellular matrix protein 1 isoform 1 precursor gi|23270687 Extracellular matrix protein 1, isoform 1 precursor gi|55958999 extracellular matrix protein 1 144 gi|27693060 Low density lipoprotein receptor-related protein 11 2 gi|55663483 low density lipoprotein receptor-related protein 11 gi|55663484 low density lipoprotein receptor-related protein 11 145 gi|16878112 Lectin, mannose-binding 2 2 146 gi|18088595 Ribonuclease, RNase A family, k6 2 gi|2135881 pancreatic ribonuclease (EC 3.1.27.5) k6 precursor - human 147 gi|4467833 cell adhesion molecule L1 2 gi|33354077 L1 cell adhesion molecule gi|27652280 L1 cell adhesion molecule gi|13435353 L1 cell adhesion molecule isoform 2 precursor gi|4557707 L1 cell adhesion molecule isoform 1 precursor 148 gi|58176768 Chain A, Zn-Alpha-2-Glycoprotein; Cho-Zag Peg 200 2 gi|7246026 Chain D, Human Zinc-Alpha-2-Glycoprotein gi|51094610 alpha-2-glycoprotein 1, zinc gi|52790422 Alpha-2-glycoprotein 1, zinc gi|38026 Zn-alpha2-glycoprotein 149 gi|292195 immunoglobulin mu chain 2 gi|21669831 immunoglobulin heavy chain VHDJ region gi|47846485 immunoglobulin heavy chain variable region gi|33319552 Ig heavy chain variable region, VH3 family gi|10636990 immunoglobulin heavy chain variable region 150 gi|51472495 PREDICTED: similar to RIKEN cDNA 1110054N06 2 151 gi|1407625 PTPsigma 2

gi|19743923 protein tyrosine phosphatase, receptor type, sigma isoform 2 precursor

gi|3702284 PTPsigma [AA 524- 1926] [Homo sapiens]

gi|19743919 protein tyrosine phosphatase, receptor type, sigma isoform 1 precursor

gi|4096822 PTPsigma-(brain)

10 152 gi|47077152 unnamed protein product 2 153 gi|22266726 LIR-D1 precursor 2 gi|15217171 CD81 partner 3 gi|55957220 immunoglobulin superfamily, member 8 gi|38197031 IGSF8 protein 154 gi|29477258 TYRO3 protein tyrosine kinase 2 gi|30704373 TYRO3 protein tyrosine kinase gi|622985 receptor tyrosine kinase gi|62088442 TYRO3 protein tyrosine kinase variant gi|7434403 receptor tyrosine kinase - human (fragment) 155 gi|22761577 unnamed protein product 2 gi|37181969 HGSC289 gi|34530413 unnamed protein product gi|37574025 PI16 protein 156 gi|37953289 insulin-like growth factor binding protein 4 2 gi|695254 insulin-like growth factor binding protein-4 gi|54696644 insulin-like growth factor binding protein 4

157 gi|21070984 peptidylglycine alpha-amidating monooxygenase isoform a, preproprotein 2

gi|21070974 peptidylglycine alpha-amidating monooxygenase isoform b, preproprotein

gi|802150 pancreatic peptidylglycine alpha-amidating monooxygenase; PAM

gi|24430388 peptidylglycine alpha-amidating monooxygenase gi|4102208 alpha-amidating monooxygenase 158 gi|55958062 inter-alpha (globulin) inhibitor, H2 polypeptide 2 gi|4504783 inter-alpha (globulin) inhibitor H2 gi|55958061 inter-alpha (globulin) inhibitor, H2 polypeptide gi|55958063 inter-alpha (globulin) inhibitor, H2 polypeptide Inter-alpha-trypsin inhibitor heavy chain H2 precursor (ITI heavy chain H2) (Inter- gi|125000 alpha-inhibitor h 159 gi|312137 fructose bisphosphate aldolase 2 gi|30582851 aldolase C, fructose-bisphosphate gi|33869380 ALDOC protein 160 gi|14149609 exostoses (multiple)-like 2 2 gi|21756514 unnamed protein product gi|23271911 EXTL2 protein 161 gi|17226298 collagen XVIII 2 gi|18765746 alpha 1 type XVIII collagen isoform 3 precursor gi|62022601 Alpha 1 type XVIII collagen, isoform 2 precursor gi|40231528 type XVIII collagen short variant gi|21708149 Similar to collagen, type XVIII, alpha 1 162 gi|7705157 CD44R4 2

gi|10432371 dJ68D18.2.5 (CD44 antigen (homing function and Indian blood group system))

gi|10432370 dJ68D18.2.4 (CD44 antigen (homing function and Indian blood group system))

gi|48255935 CD44 antigen isoform 1 precursor

gi|10432373 dJ68D18.2.2 (CD44 antigen (homing function and Indian blood group system))

11 Human Complement Regulatory Protein Cd59 (Extracellular Region, Residues 1 - 70) 163 gi|515119 2 (Nmr, 10 Structures

CD59 antigen p18-20 (antigen identified by monoclonal 16.3A5, EJ16, gi|30583047 EJ30, EL32 and G344)

Cd59 Complexed With Glcnac-Beta-1,4-(Fuc-Alpha-1,6)- Glcnac-Beta-1 (Nmr, 10 gi|640301 Structures) 164 gi|437363 14-3-3n 2 gi|47678755 YWHAH gi|46250404 YWHAZ protein gi|30354619 YWHAZ protein gi|39645797 Unknown (protein for IMAGE:6180974) 165 gi|51477716 mannosidase, alpha, class 2A, member 2 2 gi|1132479 alpha mannosidase II isozyme 166 gi|825681 inter-alpha-trypsin inhibitor C-terminal 2 gi|4504781 inter-alpha (globulin) inhibitor H1 gi|62550746 ITIH1 protein 167 gi|105387 aspartate transaminase (EC 2.6.1.1) - human 2

gi|55663625 glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1)

168 gi|18028281 NPDC-1 protein 2 gi|55962688 neural proliferation, differentiation and control, 1 gi|9050060 NPDC-1 gi|22760471 unnamed protein product gi|55962689 neural proliferation, differentiation and control, 1 169 gi|8923253 O-linked mannose beta1,2-N-acetylglucosaminyltransferase 2 gi|10434295 unnamed protein product gi|37182306 DDWK746 gi|55666407 novel protein gi|55666406 novel protein 170 gi|56203361 OTTHUMP00000028643 2 gi|37181935 SEZ6L gi|4886439 hypothetical protein gi|14133225 KIAA0927 protein gi|47678679 SEZ6L 171 gi|758781 macrophage-colony stimulating factor gamma precursor 2 gi|187463 macrophage colony-stimulating factor gi|27262663 colony stimulating factor 1 isoform b precursor gi|508986 macrophage colony-stimulating factor gi|55664932 colony stimulating factor 1 (macrophage) 172 gi|48146185 LY6H 2 gi|4505051 lymphocyte antigen 6 complex, locus H 173 gi|423113 - human 2 gi|3063520 TESTICAN

gi|62088982 sparc/, cwcv and kazal-like domains precursor variant

174 gi|189386 oligodendrocyte-myelin glycoprotein 2 gi|23106 oligodentrocyte-myelin glycoprotein gi|35145 oligodendrocyte-myelin glycoprotein 175 gi|11125772 myristoylated alanine-rich protein kinase C substrate 2 gi|45751590 MARCKS protein

12 gi|56203645 myristoylated alanine-rich protein kinase C substrate gi|187387 myristoylated alanine-rich C-kinase substrate 176 gi|182424 alpha-fibrinogen precursor 2 gi|4033511 fibrinogen alpha subunit gi|13591823 fibrinogen alpha chain preproprotein, isoform alpha gi|223068 fibrin alpha N term fragment gi|4503689 fibrinogen, alpha chain isoform alpha-E preproprotein 177 gi|14278127 Chain A, Ribonuclease 1 Des1-7 Crystal Structure At 1.9a 2 gi|1087119 pancreatic ribonuclease; HP-RNase gi|35281 pancreatic ribonuclease gi|4506547 pancreatic ribonuclease precursor gi|488413 pancreatic ribonuclease 178 gi|425518 anti-colorectal carcinoma heavy chain 2 179 gi|15215308 Dystroglycan 1, precursor 2 gi|4758116 dystroglycan 1 precursor serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), 180 gi|4507377 2 member 7

serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), gi|2780174 member 7 181 gi|182292 coagulation factor XII precursor 2 gi|180361 human factor XII gi|903736 coagulation factor XII gi|24899162 coagulation factor XII-Mie gi|15214537 F12 protein Chain B, Crystal Structure Of Hgstp1-1[v104] Complexed With The Gsh Conjugate Of 182 gi|5822570 2 (+)-Anti-Bpde gi|39654104 Chain B, Glutathione Transferase Mutant Chain B, A Folding Mutant Of Human Class Pi Glutathione Transferase, Created By gi|34811304 Mutating Aspartate 1

Chain B, A Folding Mutant Of Human Class Pi Glutathione Transferase, Created By gi|23200509 Mutating Glycine 146 gi|11514449 Chain B, Crystal Structure Of Pi Class Glutathione Transferase 183 gi|56206313 calcium binding protein Cab45 precursor (Cab45) 2 gi|56206314 calcium binding protein Cab45 precursor (Cab45) gi|5802176 calcium binding protein precursor gi|56206315 calcium binding protein Cab45 precursor (Cab45) gi|56206312 calcium binding protein Cab45 precursor (Cab45) gi|22761383 unnamed protein product 184 gi|33991465 PSMD1 protein 2 gi|1808578 proteasome subunit p112 gi|28839604 PSMD1 protein gi|33875930 PSMD1 protein gi|39963586 PSMD1 protein 185 gi|37183258 cerebellin 2 186 gi|4505375 neogenin homolog 1 2 gi|2078518 neogenin 187 gi|12698684 Ly-6 neurotoxin-like protein Lynx1 2 gi|29294641 Ly-6 neurotoxin-like protein 1 isoform c 188 gi|179704 complement component C6 precursor peptide 2 gi|23273482 C6 protein

13 gi|618466 complement component C6 gi|38488662 complement component 6 189 gi|183122 insulin-like growth factor II precursor 2 gi|33048 unnamed protein product gi|2135956 insulin-like growth factor II, domains A-E - human gi|33044 insulin-like growth factor II precursor gi|755742 unnamed protein product 190 gi|3451335 F22162_1 2 gi|46329698 IGSF4C protein gi|21686977 immunoglobulin superfamily, member 4C 191 gi|48146981 NOV 2 gi|19743680 NOVH protein gi|15929146 Nov, precursor

192 gi|1942821 Chain C, Human Aspartylglucosaminidase Complex With Reaction Product 2

193 gi|38016947 complement component 5 2 gi|179692 complement component C5 gi|68769 complement C5 precursor [validated] - human 194 gi|179726 C9 complement protein 2 gi|2258128 complement 9 gi|18088821 Complement component 9 195 gi|37181793 IGSF4 2 gi|28422552 Similar to immunoglobulin superfamily, member 4 gi|29170547 secretory isoform of TSLC-1 gi|22761688 unnamed protein product gi|4519602 IGSF4 EDC1, HI30=urinary proteinase inhibitor {N-terminal} [human, urine, Peptide Partial, 196 gi|262428 2 28 aa, segment 197 gi|10433260 unnamed protein product 2 198 gi|61656640 VPS10 domain receptor protein SORCS 3 (SORCS3) 2 199 gi|28207867 unnamed protein product 2

gi|51493162 PREDICTED: similar to gene model 895; gene model 895, (NCBI)

200 gi|51105889 retinoic acid receptor responder (tazarotene induced) 2 2 201 gi|49456613 PENK 2 202 gi|58801254 MEGF8 2 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase 203 gi|57210053 1.7 inhibitor) gi|31189 unnamed protein product Chain B, Orientation In Solution Of Mmp-3 Catalytic Domain And N- Timp-1 From gi|34811011 Residual Dipolar Coupl gi|13937969 TIMP1 protein tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase gi|57210052 inhibitor) 204 gi|4505643 procollagen C-endopeptidase enhancer 1.7 gi|51094573 procollagen C-endopeptidase enhancer gi|3135316 PCOLCE 205 gi|34734066 fibulin 1 isoform D 10.14 gi|56202438 OTTHUMP00000028589 gi|30581038 Fibulin-1 precursor

14 gi|1621019 fibulin-1D 206 gi|55662226 fructose-1,6-bisphosphatase 2 1.52 gi|2154755 fructose-1,6-bisphosphatase 2 207 gi|12654031 KAT3 protein 1.52 gi|57209364 novel protein gi|57209369 novel protein gi|56713254 kynurenine aminotransferase III isoform 1 gi|57209365 novel protein 208 gi|231098 Thioredoxin (Reduced Form) 1.52

gi|1827675 Human Thioredoxin Mutant With Cys 73 Replaced By Ser (Reduced Form)

Human Thioredoxin Double Mutant With Cys 32 Replaced By Ser And Cys 35 gi|1827674 Replaced By Ser gi|9508997 thioredoxin gi|2392150 Human Thioredoxin (D60n Mutant, Reduced Form) 209 gi|51095168 reelin 1.52 gi|51095167 reelin gi|20139420 Reelin precursor gi|30172691 unknown 210 gi|62088606 ecotropic viral integration site 5 variant 1.52 gi|51458605 PREDICTED: similar to EVI-5 homolog gi|52630438 ecotropic viral integration site 5 gi|56204495 ecotropic viral integration site 5 gi|3095098 truncated EVI5 211 gi|4240149 KIAA0830 protein 1.52 gi|20072181 KIAA0830 protein 212 gi|46102535 POT1 and TIN2 interacting protein 1.52 gi|10435745 unnamed protein product 213 gi|21359943 rhomboid family 1 1.52 gi|10438710 unnamed protein product gi|14336678 unknown 214 gi|33519447 neuroblastoma, suppression of tumorigenicity 1 precursor 1.52 gi|56203285 neuroblastoma, suppression of tumorigenicity 1 215 gi|51473065 PREDICTED: hypothetical protein XP_498651 1.52 216 gi|62020369 EPHA4 protein 1.52 gi|62420276 unknown gi|4758280 ephrin receptor EphA4 217 gi|435756 lysosomal membrane glycoprotein lamp-2 homolog 1.52 gi|12804215 LAMP2 protein gi|45550060 lysosomal-associated membrane protein 2C gi|4504957 lysosomal-associated membrane protein 2 precursor gi|307110 lysosomal membrane glycoprotein-2 218 gi|5689459 KIAA1061 protein 1.52 gi|54792136 follistatin-like 4 gi|18999423 FSTL4 protein 219 gi|52545870 hypothetical protein 1.52 gi|56204779 novel protein

15