Supporting Information for Proteomics DOI 10.1002/pmic.200600568 Xiao-Li Wang, Alex Fu, Sreekumar Raghavakaimal and Hon-Chi Lee Proteomic analysis of vascular endothelial cells in response to laminar shear stress ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Table A. Proteins altereations after 10 minutes of shear stress Accesion # Protein Name H:L* Matched Sequence Charge Score Confidence % Error Peptide Number gi|39931056 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1 (DXP reductoisomerase 1) 3.78 QNGCR 2 21 75 1.6 2 gi|14548081 28 kDa and 33 kDa Inner dynein arm light chain, axonemal (p28, p33) 2.86 CEAIEK 2 32 90 3.7 3 gi|1723793 3 beta-hydroxysteroid dehydrogenase 0.21 VKIVCAYR 2 28 90 5.9 2 gi|32171609 30S ribosomal protein S11 2.17 GCAHIK 2 33 90 6.2 4 gi|34222742 30S ribosomal protein S2 0.41 REYNAVAECHK 3 20 75 1.3 4 gi|26399495 30S ribosomal protein S5P 0.19 GCGSWEZGZGRPHTVALK 3 25 75 1 4 gi|3929352 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase) 0.07 GCSVITR 2 23 75 3.2 4 gi|23396668 3-isopropylmalate dehydratase small subunit (Isopropylmalate isomerase) 0.46 AAGVSCVIAK 2 25 75 1.3 3 gi|3123178 50S ribosomal protein L32 (Ribosomal protein I) (BL37) 2.17 ACGTYK 2 32 90 6.2 2 gi|135758 Acetyl-CoA acetyltransferase (Acetoacetyl-CoA thiolase) 0.31 VCASAMK 2 20 75 1.2 3 gi|14194435 ADAM 11 precursor (A disintegrin and metalloproteinase domain 11) 0.23 GSCGRK 2 24 75 4 2 gi|6174971 Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) 2.86 GCAQALK 2 32 90 3.7 3 gi|3913952 Adenylate kinase (ATP-AMP transphosphorylase) 0.23 GTQCAK 2 20 75 0.6 4 gi|6647402 Alanine racemase 2.86 ECALQK 2 32 90 3.7 3 gi|730039 Alpha-1,3-mannosyltransferase MNN1 6.47 ASAGACGGYIWZATHK 3 33 90 0.8 2 gi|2497468 AP-1-like transcription factor 0.15 AKCSEK 2 20 75 3.8 3 gi|2498144 Apolipophorins precursor (Contains: APOLP-1; APOLP-2) 8.26 HCTDIK 2 26 75 1.1 2 gi|1351967 Aquaporin 4 (WCH4) (Mercurial-insensitive water channel) (MIWC) 0.26 ZGPPCSR 2 20 75 7.4 2 gi|13123999 Arginyl-tRNA--protein transferase 1 0.17 VFCAR 2 21 75 4 4 gi|17432914 ATP-binding cassette, sub-family G, member 8 (Sterolin-2) 2.86 QCANTR 2 32 90 3.7 3 gi|25090065 ATP-dependent helicase DDX1 (DEAD box protein 1) 0.19 HYSCVZLHGDRKPQER 3 25 75 1 4 gi|33112387 Axoneme-associated protein mst101(3) 2.86 KCAELAK 2 32 90 3.7 3 gi|5921178 Bloom's syndrome protein homolog (mBLM) 3.66 GGSTTCRK 2 22 75 3.6 3 gi|22095546 Cadherin EGF LAG seven-pass G-type receptor 1 precursor 2.86 AGCASQR 2 32 90 3.7 3 gi|20137454 Caspase recruitment domain protein 10 0.22 CLPSSR 2 20 75 7 2 gi|1350651 Chloroplast 50s ribosomal protein L4 0.46 EIYCG 2 23 75 5.2 2 gi|18202613 Chromosome-associated kinesin KLP1 (Chromokinesin) 3.71 MCGZRK 2 29 90 1.3 4 gi|119765 Coagulation factor VII (Serum prothrombin conversion accelerator) 0.28 SYIZFCPDGFEGR 3 22 75 2.3 2 gi|124411 Colicin M immunity protein (Microcin M immunity protein) 0.34 SCGDFMK 2 40 99 4.5 4 gi|117422 Crumbs protein precursor (95F) 0.27 CPNGYK 2 20 75 5.7 2 gi|1169263 Defensin 5.58 GGRCVNTIZNZR 3 24 75 0.8 3 gi|2494282 Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1) 9.39 GGSGPPCAZR 2 33 90 3.8 4 gi|1174738 DNA topoisomerase 2.86 CEHAQIK 2 32 90 3.7 3 gi|729352 DNA43 protein 0.15 CGSPINISLHK 2 41 99 6.3 3 gi|401016 DNA-directed RNA polymerase subunit A' 2.86 CEALEK 2 32 90 3.7 3 gi|137797 E7 protein 2.86 CEATLR 2 32 90 3.7 3 gi|119180 Elongation factor 3A (EF-3A) (EF-3) 0.02 YGIZGPNGCGK 2 20 75 3.6 2 gi|21264129 Excinuclease ABC subunit 0.22 CAGPZVK 2 22 75 6.5 2 gi|30581063 Fibulin-1 precursor (Basement-membrane protein 90) (BM-90) 0.42 ZZHZCMLGK 3 39 99 0.6 3 gi|113001 Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding protein) 0.37 IVGPSGAAVPCK 2 33 90 2.1 4 gi|32129530 Filamin C (Gamma-filamin) 0.06 CSGPGLGAGVR 2 49 99 5.2 3 gi|3122339 Galectin-1 (Beta-galactoside-binding lectin L-14-I) 0.28 DDNNLCLHFNPR 3 24 75 2.3 3 gi|20138165 GC-rich sequence DNA-binding factor homolog 0.10 GERTISQLENFCR 3 21 75 2.1 3 gi|130466 Genome polyprotein 0.02 TCGAPPZR 2 22 75 2.3 4 gi|1169883 Glucocorticoid receptor (GR) 0.22 NCPAZR 2 20 75 7 2 gi|21759144 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 0.17 FVCAR 2 21 75 4 4 gi|17380211 Glutamate 5-kinase (Gamma-glutamyl kinase) (GK) 2.86 QCAELK 2 32 90 3.7 3 gi|462162 Guanine nucleotide-binding protein alpha-4 subunit (G alpha 4) 0.06 EIVNCDYFK 3 43 99 0.9 2 gi|140581 H repeat-associated protein ydcC (ORF-H) 3.62 GKIITTDAMGCQK 3 26 75 2.2 2 gi|122134 H-2 class I histocompatibility antigen, q8 alpha chain precursor 3.71 ETLLCTDPPK 3 43 99 0.4 2 gi|399997 Homeobox protein Hox-B1 (Ghox-lab) 0.10 DPACPSEPZPNASRAR 3 21 75 2.1 3 gi|22001687 Homoserine kinase (HK) 0.03 CVSAVHR 2 22 75 1.8 2 gi|2498452 Imidazole glycerol phosphate synthase subunit hisF (IGP synthase cyclase subunit) 0.27 HTAVCG 2 22 75 0.4 4 gi|21431575 Insulin receptor-related protein precursor (IRR) 2.86 CEGLZPK 2 32 90 3.7 3 gi|26395479 Interleukin-1 receptor-like 2 precursor (IL-1Rrp2) 0.30 CNAATGLITP 2 24 75 1.6 2 gi|6016387 Isopenicillin N synthetase (IPNS) (Isopenicillin N synthase) 9.32 RZCZGASR 2 22 75 6.2 3 gi|6016488 L-lactate dehydrogenase C chain (LDH-C) (LDH testis subunit) (LDH-X) 0.45 VFGSGCNLDSAR 3 20 75 12.6 3 gi|38257899 LysM-domain GPI-anchored protein 2 precursor 0.26 ACSSSVRK 2 22 75 0.5 4 gi|1708892 Lysozyme precursor (1,4-beta-N-acetylmuramidase) 0.23 ASKCAK 2 20 75 0.6 4 gi|1718104 Major capsid protein (MCP) 2.86 ACGAGVNVK 2 32 90 3.7 3 gi|547903 Metabotropic glutamate receptor 6 precursor (mGluR6) 2.86 ACGALKK 2 32 90 3.7 3 gi|8928207 Metallothionein (MT) (AnMT) 0.20 GGSSEKCSZZN 3 22 75 0.4 2 gi|2497900 Metallothionein-like protein type 0.17 ZGSSCK 2 21 75 4 4 gi|2497517 Mevalonate kinase (MK) 0.02 IFNCRMMN 2 20 75 3.6 2 gi|24211982 Midasin (MIDAS-containing protein) 0.15 SZCSSK 2 20 75 2.1 2 gi|30315970 Mineralocorticoid receptor (MR) 0.22 NCPAZR 2 20 75 7 2 gi|139160 Morphogenetic protein (p12 protein) 5.85 KPEVEVQAAPFTCR 3 20 75 0.9 2 gi|38257869 NAD-dependent deacetylase (Regulatory protein SIR2 homolog) 3.71 CMGZER 2 29 90 1.3 4 gi|115422 Neural-cadherin precursor (N-cadherin) (Cadherin-2) 18.24 MCRIAGTPPR 3 52 99 4.8 3 gi|129168 Oncostatin M precursor (OSM) 3.78 LEGCR 2 21 75 1.6 2 gi|37999492 Patched protein homolog 2.43 NYFDVCPHIDR 3 30 90 4.4 4 gi|548630 Peptide transporter PTR2 (Peptide permease PTR2) 0.41 CWLIAIVELSER 3 20 75 1.3 4 gi|6919841 Phorbol-12-myristate-13-acetate-induced protein 1 (PMA-induced protein 1) 0.26 LFCSGT 2 21 75 5.4 3 gi|20139379 Phosphate-binding protein 3 precursor (PBP-3) (PstS-3) (Antigen Ag88) 0.08 VDCGGK 2 22 75 0.8 2 gi|24638082 Phospholipase A2 (Phosphatidylcholine 2-acylhydrolase) 0.15 FKHTDACZR 2 28 90 6.3 3 gi|130588 POL polyprotein [Contains: Reverse transcriptase ; Endonuclease] 0.42 RGAYCLWK 3 39 99 0.6 3 gi|112711 Potential 194 kDa protein (putative replicase) [contains: 134 kDa protein] 0.29 CNNTYQGZTZR 3 22 75 5.3 3 gi|30316371 Potential phospholipid-transporting ATPase ID (ATPase class I type 8B member 2) 4.48 MFCMK 2 27 75 5.4 4 gi|549719 Probable beta-adaptin (Clathrin assembly protein large beta chain) 0.46 TAVICVAK 2 20 75 1.3 4 gi|13124065 Probable calcium-binding mitochondrial carrier F55A11.4 3.71 EGIRCFYK 3 43 99 0.4 2 gi|13124698 Probable calcium-binding mitochondrial carrier YNL083W 3.78 LEGCR 2 21 75 1.6 2 gi|267105 Probable large tegument protein 0.29 TLLSICPK 2 25 75 3.1 4 gi|2495391 Probable nitrogen assimilation transcriptional activator 2.86 CGALTVK 2 32 90 3.7 3 gi|2833610 Probable precorrin-3B C17-methyltransferase (Precorrin-3 methyltransferase) 2.35 VDLIVCYK 2 26 75 2.3 2 gi|6647879 Probable tRNA modification GTPase trmE 4.19 AFVCVSAK 2 37 99 0.5 2 gi|2501463 Probable ubiquitin carboxyl-terminal hydrolase FAF-X 2.29 ILDYSCSQDR 3 35 99 4.5 4 gi|130976 Profilin 2.33 CYEMASHLR 3 23 75 4.3 2 gi|12644100 Progesterone receptor (PR) 0.22 NCPAZR 2 20 75 7 2 gi|730305 Prostaglandin-H2 D-isomerase precursor (Lipocalin-type prostaglandin D synthase) 0.46 FTAFCK 2 20 75 5.2 2 gi|400137 Protein kinase C, zeta type (nPKC-zeta) 0.35 GAYCGQZSER 2 36 99 4.9 3 gi|1718018 Protein U59 4.08 EMVSCIWK 3 57 99 0.5 4 gi|12230486 Protein-arginine deiminase type I (Peptidylarginine deiminase I) 0.17 VFCAR 2 21 75 4 4 gi|6226890 Protein-tyrosine phosphatase 0.37 QTTNCZYR 3 20 75 0.4 3 gi|37999834 Protocadherin gamma A9 precursor (PCDH-gamma-A9) 0.38 CLVNFK 2 24 75 11 3 gi|1345982 Putative FERT-1 protein 4.49 CGVALLPSGA 2 25 75 3.6 3 gi|6094277 Putative hexulose-6-phosphate isomerase (HUMPI) 2.25 MQEAGFIC 2 21 75 1.2 3 gi|1730602 Putative vitellogenin receptor precursor (Yolkless protein) (YL) 2.86 KCALGAK 2 32 90 3.7 3 gi|6685820 PyrBI protein 3.78 LEGVCR 2 21 75 1.6 2 gi|7388019 Pyruvate,phosphate dikinase (Pyruvate,orthophosphate dikinase) 2.86 QCALQK 2 32 90 3.7 3 gi|21903444 Raf homolog serine 0.26 CASSSIDR 2 22 75 0.5 4 gi|132608 Ribonucleoside-diphosphate reductase M1 chain ) 2.86 QCALISK 2 32 90 3.7 3 gi|37538006 RING-box protein 2 (Rbx2) (RING finger protein 7) 2.86 CQAENK 2 32 90 3.7 3 gi|1346520 S-adenosylmethionine synthetase 3.78 KNGTCR 2 21 75 1.6 2 gi|1346361 Serine/threonine-protein kinase shk2 0.46 TFCFK 2 20 75 5.2 2 gi|11387093 Serotonin N-acetyltransferase (Aralkylamine N-acetyltransferase) (AA-NAT) 0.22 CLPZAR 2 20 75 7 2 gi|136191 Serotransferrin precursor (Transferrin) 4.20 SVIPSDGPSVACVK 3 20 75 1 4 gi|6094381 SOX-15 protein (SOX-20 protein) (SOX-12 protein) 0.27 SSGAGPSRCGQGR 3 23 75 0.7 2 gi|19863446 Splicing factor 3B subunit 3 2.81