Supporting Information for Proteomics DOI 10.1002/pmic.200401336 Ilan Beer, Eilon Barnea, Arie Admon Centralized data analysis of a large interlaboratory proteomics project-A feasibility study ª 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Number Number Amino Number of high IPI of acid Protein name of labs quality peptides coverage spectra IPI00022229.1 236 8 3490 59 Apolipoprotein B-100 precursor IPI00164623.2 151 8 12671 82 IPI00032257.1 150 4 12628 83 complement component 3 precursor IPI00022434.1 110 8 13599 94 Serum albumin precursor Complement C4 precursor [Contains: C4A IPI00032258.2 99 8 5449 58 anaphylatox IPI00022463.1 94 8 9905 82 Serotransferrin precursor IPI00032256.1 92 8 15676 67 Alpha-2-macroglobulin precursor IPI00328461.1 84 8 2103 51 Hypothetical protein DKFZp686H112 Complement C5 precursor [Contains: C5a IPI00032291.1 74 6 591 50 anaphylatox IPI00179357.1 68 8 20 2 Titin IPI00017601.1 66 8 3910 65 Ceruloplasmin precursor IPI00029739.1 65 8 2265 57 Splice isoform 1 of P08603 IPI00182635.1 65 8 1358 46 IPI00220327.1 56 7 4729 61 keratin 1 IPI00021841.1 51 8 7728 91 Apolipoprotein A-I precursor IPI00019580.1 51 6 701 67 Plasminogen precursor IPI00025426.1 48 4 3184 38 Pregnancy zone protein precursor IPI00021304.1 48 4 2241 68 Keratin, type II cytoskeletal 2 epidermal IPI00013933.1 48 4 59 20 Splice isoform DPI of P15924 IPI00294193.1 46 8 1916 56 Splice isoform 1 of Q14624 IPI00021885.1 45 7 1811 45 Splice isoform Alpha-E of P02671 IPI00305457.1 44 8 5917 76 Alpha-1-antitrypsin precursor Splice isoform 2 of Q14624 Inter-alpha- IPI00218192.1 44 2 1880 55 trypsin inh IPI00177988.1 44 6 1289 56 complement factor B preproprotein Fibrinogen beta chain precursor [Contains: IPI00298497.1 43 6 1505 65 Fibrino IPI00019571.1 41 8 3844 70 Haptoglobin-2 precursor Inter-alpha-trypsin inhibitor heavy chain H2 IPI00305461.1 40 8 1625 42 precu IPI00019943.1 40 7 570 53 Afamin precursor IPI00019568.1 39 8 1008 66 Prothrombin precursor IPI00298853.1 38 8 3678 67 Vitamin D-binding protein precursor IPI00304273.1 38 8 1010 75 Apolipoprotein A-IV precursor IPI00295684.1 37 5 3097 60 Keratin 10 IPI00240020.1 37 6 618 52 keratin 6A IPI00022937.1 37 4 93 19 Coagulation factor V precursor IPI00023014.1 37 2 53 17 Von Willebrand factor precursor IPI00019359.1 36 5 2095 55 Keratin, type I cytoskeletal 9 IPI00032179.1 36 8 1410 68 Antithrombin-III precursor IPI00032328.1 36 8 876 51 Splice isoform HMW of P01042 IPI00300725.1 36 1 621 51 keratin 6C IPI00218819.1 35 3 631 65 keratin 14 IPI00296099.1 35 3 223 37 Thrombospondin 1 precursor Inter-alpha-trypsin inhibitor heavy chain H1 IPI00292530.1 34 8 1392 41 precu IPI00293665.1 34 1 593 49 keratin 6B IPI00296608.1 34 3 177 49 complement component 7 precursor IPI00021891.3 33 6 1337 77 Splice isoform Gamma-B of P02679 IPI00009920.1 33 6 256 41 Complement component C6 precursor Splice isoform LMW of P01042 Kininogen IPI00215894.1 32 3 860 64 precursor IPI00026314.1 32 4 476 48 Gelsolin precursor, plasma IPI00008558.1 32 5 198 60 Plasma kallikrein precursor IPI00007240.1 32 4 163 61 Coagulation factor XIII B chain precursor IPI00303963.1 31 3 199 47 Complement C2 precursor IPI00291867.1 30 4 361 55 Complement factor I precursor Splice isoform 2 of O75882 Attractin IPI00162735.1 30 5 138 28 precursor IPI00022488.1 29 8 3238 53 Hemopexin precursor IPI00032215.1 29 8 3180 74 Alpha-1-antichymotrypsin precursor IPI00021842.1 29 6 584 75 Apolipoprotein E precursor IPI00009867.1 29 2 546 41 Keratin, type II cytoskeletal 5 Inter-alpha-trypsin inhibitor heavy chain H3 IPI00028413.1 29 4 185 40 precu IPI00178741.1 28 8 1406 51 Hypothetical protein IPI00021727.1 28 6 864 57 C4b-binding protein alpha chain precursor IPI00217963.1 28 2 550 56 keratin 16 IPI00296165.1 28 4 332 44 Complement C1r component precursor IPI00296170.1 27 4 2590 55 Haptoglobin-related protein precursor IPI00165243.1 27 2 1380 46 Hypothetical protein IPI00292950.1 27 5 589 56 Heparin cofactor II precursor IPI00017696.1 27 4 261 45 Complement C1s component precursor IPI00152302.1 26 8 2452 58 Hypothetical protein IPI00244103.1 26 4 196 54 Hypothetical protein FLJ38023 IPI00022371.1 25 7 492 48 Histidine-rich glycoprotein precursor IPI00182655.1 25 3 59 42 keratin, hair, basic, 6 IPI00182654.1 25 1 58 40 Keratin IPI00239405.1 25 7 4 3 Splice isoform 1 of Q8WXH0 IPI00169423.1 23 8 3164 45 Hypothetical protein FLJ14473 Factor VII active site mutant IPI00328111.1 23 1 1944 38 immunoconjugate IPI00291866.1 23 8 835 49 Plasma protease C1 inhibitor precursor IPI00291262.1 23 8 775 46 Clusterin precursor Complement component C8 beta chain IPI00294395.1 23 3 193 49 precursor Insulin-like growth factor binding protein IPI00020996.1 23 3 185 48 complex Phosphatidylinositol-glycan-specific IPI00299503.1 23 4 55 31 phospholipase IPI00166866.1 22 1 3131 48 Hypothetical protein IPI00179358.1 22 3 387 55 IPI00022395.1 22 4 277 47 Complement component C9 precursor Complement component C8 alpha chain IPI00011252.1 22 4 210 47 precursor IPI00294004.1 22 6 168 33 Vitamin K-dependent protein S precursor IPI00298828.1 21 7 708 67 Beta-2-glycoprotein I precursor IPI00185744.1 21 1 267 64 IPI00166729.1 21 8 227 59 Alpha-2-glycoprotein 1, zinc IPI00029168.1 21 2 102 6 Apolipoprotein IPI00297795.1 21 1 55 36 Type II intermediate filament of hair keratin IPI00060961.1 20 1 3095 40 Hypothetical protein FLJ25298 IPI00168728.1 20 7 1381 40 FLJ00385 protein IPI00003351.1 20 2 93 46 Extracellular matrix protein 1 precursor IPI00008556.1 20 3 34 43 Splice isoform 1 of P03951 IPI00061977.1 19 2 2587 36 Hypothetical protein IPI00022910.1 19 7 1022 58 Ig mu heavy chain disease protein IPI00029863.1 19 7 290 46 Alpha-2-antiplasmin precursor Human full-length cDNA 5-PRIME end of IPI00328609.1 19 3 160 46 clone CS0DM0 IPI00019581.1 19 4 127 37 Coagulation factor XII precursor IPI00292946.1 19 4 123 49 Thyroxine-binding globulin precursor IPI00004608.1 18 6 1132 58 Ig gamma-2 chain C region IPI00216722.1 18 8 1012 45 alpha 1B-glycoprotein IPI00298971.1 18 7 522 45 Vitronectin precursor IPI00006114.2 18 5 301 50 Pigment epithelium-derived factor precursor IPI00025276.1 18 2 22 5 Splice isoform XB of P22105 IPI00010471.1 18 1 19 40 L-plastin IPI00021406.1 18 7 5 5 Sacsin IPI00004641.1 17 5 1710 53 Ig alpha-2 chain C region IPI00163207.1 17 6 297 49 Peptidoglycan recognition protein L precursor IPI00163628.2 17 7 196 18 IPI00023750.1 17 5 154 45 Splice isoform 1 of O14791 IPI00025204.1 17 5 125 59 CD5 antigen-like precursor IPI00032513.1 17 3 94 50 Keratin, type I Hepatocyte growth factor-like protein IPI00292218.1 17 3 40 31 precursor IPI00025879.1 17 3 11 12 Myosin heavy chain, skeletal muscle, adult 1 IPI00009286.1 17 5 2 4 Splice isoform 1 of Q03164 IPI00020091.1 16 8 1138 68 Alpha-1-acid glycoprotein 2 precursor Angiotensinogen precursor [Contains: IPI00032220.1 16 8 715 41 Angiotensin I IPI00020986.2 16 6 281 58 Lumican precursor IPI00009866.1 16 1 254 32 Keratin, type I cytoskeletal 13 IPI00166930.1 16 3 166 34 Similar to RIKEN cDNA 1300018K11 gene Glutamate carboxypeptidase-like protein 2 IPI00064667.1 16 4 110 41 precurso IPI00296534.1 16 1 90 31 Splice isoform D of P23142 Splice isoform B of P23142 Fibulin-1 IPI00218803.2 16 2 89 33 precursor IPI00171678.1 16 2 85 37 Dopamine beta-hydroxylase IPI00031423.1 16 1 70 52 Keratin, type I cuticular HA3-II IPI00003590.1 16 3 44 25 Quiescin IPI00032541.1 16 1 31 29 Type II intermediate filament of hair keratin IPI00298860.1 16 1 18 32 Lactotransferrin precursor IPI00306371.1 16 7 8 3 IPI00303335.1 16 7 2 2 Nebulin IPI00178276.1 15 8 2427 68 IPI00022895.2 15 4 640 36 Alpha-1B-glycoprotein precursor Splice isoform C of P23142 Fibulin-1 IPI00296537.1 15 1 84 31 precursor IPI00220011.1 15 1 79 31 Hypothetical protein NT2RP3003649 Complement-activating component of Ra- IPI00299307.1 15 2 52 28 reactive fac IPI00290283.1 15 2 37 28 Complement factor MASP-3 IPI00001753.1 15 7 12 10 Myosin heavy chain, skeletal muscle, fetal IPI00007856.1 15 1 9 10 Myosin heavy chain, skeletal muscle, adult 2 IPI00186711.1 15 3 7 3 IPI00022429.1 14 8 2059 58 Alpha-1-acid glycoprotein 1 precursor IPI00022432.1 14 7 1942 76 Transthyretin precursor IPI00166489.1 14 3 918 54 Hypothetical protein IPI00154742.1 14 8 890 53 Hypothetical protein IPI00102937.1 14 5 832 49 Hypothetical protein IPI00004617.1 14 4 749 53 Ig gamma-3 chain C region IPI00218816.1 14 6 518 90 beta globin IPI00005859.1 14 3 343 17 Cytokeratin type II AMBP protein precursor [Contains: Alpha-1- IPI00022426.1 14 5 341 51 microglo IPI00184978.1 14 1 277 31 IPI00041065.2 14 6 120 26 hyaluronan binding protein 2 IPI00022417.2 14 8 112 51 Leucine-rich alpha-2-glycoprotein precursor IPI00025864.1 14 2 85 30 Cholinesterase precursor IPI00329775.1 14 3 72 37 Carboxypeptidase B2 IPI00005864.1 14 3 45 37 Prenylcysteine oxidase precursor Protein Z-dependent protease inhibitor IPI00007199.1 14 2 39 36 precursor asp (abnormal spindle)-like, microcephaly IPI00296362.1 14 6 30 5 associat IPI00003362.1 14 4 20 29 78 kDa glucose-regulated protein precursor IPI00014898.1 14 1 7 3 Splice isoform 1 of Q15149 IPI00178229.1 13 4 2455 62 IPI00021854.1 13 8 1723 74 Apolipoprotein A-II precursor IPI00022431.1 13 8 1365 35 Alpha-2-HS-glycoprotein precursor IPI00178482.1 13 2 898 52 Hypothetical protein IPI00168679.1 13 3 857 52 Hypothetical protein IPI00008359.1 13 1 184 11 Keratin, type II cytoskeletal 2 oral IPI00290857.1 13 7 183 12 Keratin, type II cytoskeletal 3 IPI00178926.1 13 8 92 62 Hypothetical protein IPI00021439.1 13 5 78 39 Actin, cytoplasmic 1 IPI00218413.1