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Supporting Information for Proteomics DOI 10.1002/Pmic.200700455

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Supporting Information for Proteomics DOI 10.1002/Pmic.200700455 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 protein 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 Actin 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 glycoprotein-2 22.62 gi|42740907 clusterin isoform 2 gi|178855 apolipoprotein 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 apolipoprotein E 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 hemopexin 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-Thrombin-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 coagulation 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 vitronectin 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 orosomucoid 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 phospholipid 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 apolipoprotein D, 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 proteins 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 ganglioside activator, precursor gi|226416 Gm2 activator protein gi|14278641 Chain
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