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 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 ) 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 ) (AdoHcyase) 2.86 GCAQALK 2 32 90 3.7 3 gi|3913952 Adenylate (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 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 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 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 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 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 (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- 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 (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: ; 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 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 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 CPIPRR 2 26 75 1.2 2 gi|25091337 StAR-related lipid transfer protein 13 (StARD13) 2.86 KCHEANK 2 32 90 3.7 3 gi|115977 T- surface antigen CD2 precursor (T-cell surface antigen T11 2.86 CKAVNR 2 32 90 3.7 3 gi|267108 Tetranectin precursor (TN) (Plasminogen-kringle 4 binding protein) 6.24 EQQALQTVCLK 3 40 99 0.4 4 gi|12644428 Thrombospondin 1 precursor 0.27 AQLYIDCEK 2 48 99 0.5 2 gi|266331 Trans-acting transcriptional protein ICP0 (P135 protein) (IER 2.9 0.05 ACSPEPR 2 30 90 1 4 gi|1174573 Transcriptional activator TAF-1 2.03 RCQPTGEINDDSEK 3 31 90 1.9 3 gi|11387048 Transforming growth factor-beta-inducible early growth response protein 2 0.42 FVZPVCDRR 3 39 99 0.6 3 gi|135952 from transposon Tn916 & Tn1545 () 0.34 ASFYIAIQDDCVRK 3 20 75 1.9 3 gi|401160 Tubulin alpha-1 chain 0.29 EVITINIGQAGCQLGNK 4 20 75 5.3 3 gi|115978 Tumor necrosis factor receptor superfamily member 8 precursor (CD30L receptor) 9.32 ZTACVSZSR 2 22 75 6.2 3 gi|6831526 Uridylate kinase (UK) (Uridine monophosphate kinase) (UMP kinase) 2.86 ECADAVR 2 32 90 3.7 3 gi|139705 Wnt-3a protein 9.32 EKCHZIF 2 22 75 6.2 3 gi|20532299 Zinc finger BED domain containing protein 0.17 CDAGSPSK 2 21 75 1.5 3 gi|28202104 Zinc finger DHHC domain containing protein 6 (H4 homolog) 0.42 MGIFCSVIK 3 39 99 0.6 3 gi|38258828 Zinc finger protein 283 0.38 CKSIFK 2 24 75 11 3 gi|20141034 Zinc finger protein 287 (Zfp-287) (Zinc finger protein SKAT-2) 9.61 ZTACGK 2 21 75 4.7 2

Functional unknown proteins: gi|134382 Zinc finger protein sdc-1 3.78 KNGCR 2 21 75 1.6 2 gi|549663 Hypothetical 50.3 kDa protein in TFA1-PAN3 intergenic region 0.23 SGCRK 2 24 75 4 2 gi|2501343 Hypothetical 59.1 kDa protein in SOK2-STB4 intergenic region 0.32 SYHSAINAYNKCK 3 20 75 1.6 2 gi|465736 Hypothetical GTP-binding protein C02F5.3 in chromosome III 0.21 CRVLPZIEZHGPR 3 24 75 1 4 gi|2497831 Hypothetical MCM-type protein MJ1489 0.41 LPAECAILAAZNPR 3 20 75 1.3 4 gi|6686189 Hypothetical protein AF1698 0.08 VZZCGGK 2 22 75 0.8 2 gi|2811027 Hypothetical protein At5g27140 3.31 TEECSKK 2 20 75 8.8 2 gi|1723518 Hypothetical protein C22E12.04 in chromosome 0.15 SZCSSK 2 20 75 2.1 2 gi|1351693 Hypothetical protein C3H1.10 in chromosome 0.45 TDTGZZSSSCCK 3 24 75 1.9 2 gi|18203028 Hypothetical protein FPV002 0.31 SWZRCFZZPZEVFLR 4 22 75 1.2 3 gi|37999512 Hypothetical protein MJ1396 5.29 SCGIYGK 2 28 90 0.9 2 gi|24418800 Hypothetical protein MJ1537 5.85 NZEECLEIFINKIK 3 20 75 0.9 2 gi|6226304 Hypothetical protein RP006 0.45 STSLCK 2 20 75 12.6 3 gi|14285875 Hypothetical protein TP0415 0.17 VFCAR 2 21 75 4 4 gi|14285946 Hypothetical protein TP0816 3.78 NQGCR 2 21 75 1.6 2 gi|2828495 Hypothetical protein yhbE (ORF1) 3.78 EIGCR 2 21 75 1.6 2 gi|21431852 Hypothetical protein ZK643.6 in chromosome III 0.03 CPATZGK 2 27 75 1.4 2 gi|33517007 Hypothetical UPF0271 protein PP4577 2.06 DLLHYQIGALDGICK 3 28 90 3.8 2 * H: sheared; L: control Table B. Proteins alterations after 3 hours of shear stress

Accesion # Protein Name H:L* Matched Sequence Charge Score Confidence % Error Peptide Number gi|38604726 3-isopropylmalate dehydratase large subunit (Isopropylmalate isomerase) 0.26 DIKAATQSAQCR 3 20 75 2.4 2 gi|2498245 4-hydroxy-2-oxovalerate aldolase (HOA) 0.22 HGCDVR 2 21 75 1.1 2 gi|14916693 60S ribosomal protein L15 & L19 2.22 HCGALR 2 20 75 1.9 2 gi|2507307 60S ribosomal protein L3 (YL1) (RP1) (Trichodermin resistance protein) 2.49 GCIPGNR 2 20 75 1.6 2 gi|133106 60S ribosomal protein L40 (CEP52) 2.43 ACGHZSNLR 3 28 90 1.6 3 gi|1173045 60S ribosomal protein L37A 4.07 KAVGIWGCK 2 25 75 3.3 3 gi|584727 Actin-depolymerizing factor 2 (Uncoordinated protein 60) 2.45 MASGVKVDPSCK 3 26 75 4 4 gi|20137548 ADAM 24 precursor (A disintegrin and metalloproteinase domain 24) (Testase 1) 0.29 SCIHR 2 27 75 0.9 4 gi|24211441 ADAM 9 precursor (A disintegrin and metalloproteinase domain 9) 2.45 DZSCGAK 2 22 75 2.6 2 gi|11131197 ADAMTS-8 precursor 7.10 ZGVCGGK 2 20 75 1 2 gi|29336566 Alanyl-tRNA synthetase (Alanine--tRNA ) (AlaRS) 2.06 CQRSLADQK 3 44 99 0.6 3 gi|23822161 Alpha-1-syntrophin (59 kDa dystrophin-associated protein A1, acidic component 1) 2.85 CTPSDPEHR 2 44 99 2.2 3 gi|1709080 Antibacterial peptide PMAP-23 precursor (Myeloid antibacterial peptide 23) 2.06 QCVGTVTLK 3 44 99 0.6 3 gi|37999913 Anti-epilepsy peptide precursor (BmK AEP) 0.02 GSNGCK 2 28 90 4 2 gi|20140219 Anti-neuroexcitation peptide II precursor (ANEPII) 0.02 GSNGCK 2 28 90 4 2 gi|12229553 Armadillo repeat protein deleted in velo-cardio-facial syndrome 3.60 DCGGVPALVR 2 30 90 2.1 3 gi|1703406 Arrestin, red cell isoform 1 (CARR) 0.05 AFCAK 2 23 75 7 3 gi|1176769 Arsenical resistance operon repressor 0.36 KGEGDCZ 2 25 75 0.6 4 gi|24636249 Asp-hemolysin precursor (Asp-HS) 2.75 YGGAIGNC 2 38 99 2.1 2 gi|1346597 Atonal protein homolog 1 (Helix-loop-helix protein mATH-1) (MATH1) 3.65 SGCGGLSK 2 22 75 4.4 4 gi|14916542 ATP-dependent CLP protease ATP-binding subunit ClpX-like 0.33 GISCGR 2 20 75 0.4 4 gi|114365 A-type inclusion protein (ATI) 4.07 CFDTNHAK 2 25 75 3.3 3 gi|23822158 Beta-2-syntrophin (59 kDa dystrophin-associated protein A1, basic component 2) 0.17 MCFAAR 2 22 75 0.9 3 gi|114214 Beta-arrestin 2 (Arrestin, beta 2) 0.05 AFCAK 2 23 75 7 3 gi|27805615 Beta-microseminoprotein J1 precursor (msp-J1) 2.03 TDNCDSZTCREK 3 29 90 1.6 3 gi|266774 B-phycoerythrin alpha chain 0.36 LCZPR 2 21 75 7.4 4 gi|13431352 Calcium-binding protein CaBP1 0.39 MGNCVK 2 20 75 3.6 2 gi|12643802 C-C chemokine receptor type 10 (C-C CKR-10) (CC-CKR-10) (CCR-10) 0.04 SCSSSKR 2 23 75 2 3 gi|28380034 Cdk5 and abl substrate 2 (Interactor with cdk3 2) (Ik3-2) 2.31 IVLICAK 2 21 75 1.6 2 gi|115914 Cell division control protein 25 0.39 DACEK 2 20 75 3.6 2 gi|1705677 Cell division control protein 48 homolog A & D 5.16 GVLFYGPPGCGK 2 43 99 1.8 4 gi|12643825 Cell division cycle 2-related protein kinase 7 0.36 ICZPR 2 21 75 7.4 4 gi|1173403 Chlorotoxin 18.19 CYGPQZLZR 3 36 99 6.5 4 gi|18202613 Chromosome-associated kinesin KLP1 (Chromokinesin) 0.41 MCGZRK 2 27 75 0.7 3 gi|26392615 Copper transport protein ctr6 (Copper transporter 6) 2.67 HCSMK 2 21 75 0.9 3 gi|116935 Core antigen 2.49 SQSPASNC 2 31 90 1.6 2 gi|38604740 CUB and sushi multiple domains protein 3 precursor 3.16 VPICEAGSKILVK 3 29 90 1.6 3 gi|2498997 Cytosolic acyl coenzyme A thioester hydrolase 7.35 CVAALAR 2 25 75 2.8 2 gi|117736 Cytotoxin homolog S3C2 0.18 ZLNTPLPLFYKTCPEGK 3 20 75 1.9 4 gi|6014946 DEAD-box RNA helicase DEAD2 (mDEAD2) (D1PAS1 related sequence 1) 4.07 GKIGLDFCK 2 25 75 3.3 3 gi|2500838 Degenerin del-1 2.08 TLGIACKPR 2 32 90 1.8 2 gi|39930965 Deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) 0.16 EACGGK 2 22 75 5.4 3 gi|13124093 Dickkopf related protein-2 precursor (Dkk-2) (Dickkopf-2) (hDkk-2) 0.05 ZDCAK 2 23 75 7 3 gi|3913526 DNA polymerase [Contains: Pho pol intein (Pho Pol I intein)] 0.48 EGCEEYDVAPK 3 32 90 5.2 3 gi|12644390 DNA polymerase epsilon, catalytic subunit A (DNA polymerase II subunit A) 0.29 SCNFZR 2 27 75 0.9 4 gi|24211655 DNA polymerase IV (Pol IV) 6.12 YCTSISVNIR 3 42 99 5.1 3 gi|1174738 DNA topoisomerase 0.48 QVAILCNHQK 3 23 75 5.2 4 gi|17865785 DNA topoisomerase III 2.06 KCVIELEIAK 3 44 99 0.6 3 gi|37999956 Downstream neighbor of Son protein (Protein 3SG) 8.33 LLNFLINCK 2 39 99 0.7 2 gi|585073 Dynein heavy chain, cytosolic (DYHC) 0.29 DCZFGVTGLK 3 23 75 0.6 3 gi|137776 E6 protein 0.46 CLIAAAKLR 3 20 75 2 2 gi|12229783 Ellis-van Creveld syndrome protein (DWF-1) 2.43 GGAACK 2 23 75 1.6 2 gi|1706631 Ephrin type-A receptor 7 precursor 2.02 GTCVSSAEEEAENSPR 3 24 75 1.8 3 gi|3024790 Excinuclease ABC subunit 0.26 DCSVPASTVZRR 3 20 75 2.4 2 gi|21542229 Exocyst complex component sec8 4.50 CNSRIIALK 2 39 99 1.8 2 gi|1706728 Exonuclease I (EXO I) 0.30 HQRVYCPK 2 20 75 0.4 4 gi|416985 Formate dehydrogenase-O, iron-sulfur subunit 2.13 LIDVTTZIGCK 3 24 75 6.1 2 gi|120628 G surface protein, allelic form 168 precursor 0.47 GAZSSYTIEEQCK 3 20 75 1.9 3 gi|21263449 G2/mitotic-specific cyclin-B1 2.12 TCSVAGPTQKPR 3 32 90 2 2 gi|2495241 GAG polyprotein [Contains: Core protein P16; Core protein P26] 0.26 CWNZGKDGHSAR 3 20 75 2.4 2 gi|2493882 Gamma crystallin M1-2 (Gamma M1-2) 0.07 RVIGIC 2 21 75 11.3 4 gi|20454925 Gamma-tubulin complex component 6 (GCP-6) 0.36 LCZPR 2 21 75 7.4 4 gi|138101 Gene 6 Protein 0.21 CETZK 2 21 75 2 2 gi|130466 Genome polyprotein (Contains: P22; GP32) 2.43 ALAACK 2 23 75 1.6 2 gi|2499563 Genome polyprotein [Contains: P1A; P1B; P1C) 0.08 CELFTYMR 3 41 99 0.6 2 gi|121398 Glp-1 protein precursor 0.39 EGCEK 2 20 75 3.6 2 gi|33301370 Glucans glucosyltransferase 0.43 ACGGAFR 2 28 90 7.4 4 gi|20141560 Glutamyl-tRNA reductase 1, chloroplast precursor (GluTR) 0.43 CDGSDSR 2 27 75 7.4 2 gi|39931372 Glutathione synthetase (Glutathione synthase) (GSH synthetase) (GSH-S) (GSHase) 0.27 QICAALAPALR 3 30 90 3.1 4 gi|115063 Glycoprotein antigen BM86 precursor (Protective antigen) 0.29 GPDGQZINACK 3 23 75 0.6 3 gi|1718170 Glycoprotein H precursor 0.49 CAKITR 2 20 75 0.3 3 gi|11387167 Glycyl-tRNA synthetase alpha chain (Glycine--tRNA ligase alpha chain) (GlyRS) 0.46 NLGFPLCHK 2 27 75 3.5 4 gi|20532126 (GMP kinase) 0.39 SVCEK 2 20 75 3.6 2 gi|13626998 Hepatocyte nuclear factor 6 (HNF-6) (One cut domain family member 1) 2.43 LAACK 2 23 75 1.6 2 gi|119871 High affinity immunoglobulin gamma Fc receptor I precursor 3.65 CHAWK 2 22 75 4.4 4 gi|21759178 Histidinol-phosphate aminotransferase (Imidazole acetol-phosphate transaminase) 0.16 DQNKQPGLANCLR 3 28 90 0.5 2 gi|417122 Histone transcription regulator 0.48 IPKICLGHK 2 35 99 1.9 3 gi|1705494 Homeobox protein box-5 (NVHBOX-5) 0.26 APHGACQTSGTLR 3 20 75 2.4 2 gi|26454638 Homeobox protein HAT3.1 3.20 SSSSACK 2 21 75 0.6 2 gi|14548079 Inhibitor of nuclear factor kappa-B kinase epsilon subunit 2.85 CVVAGMNHLR 2 44 99 2.2 3 gi|124462 Interferon-alpha 0.40 QIPDCENVK 2 24 75 2.2 4 gi|26395383 Interleukin-18 receptor 1 precursor (IL1 receptor-related protein) (IL-1Rrp) 0.00 SCIHR 2 25 75 -1 3 gi|13637587 Isocitrate (Isocitrase) (Isocitratase) (ICL) 0.29 CGHQGGK 2 22 75 0.9 3 gi|37079273 Killer cell immunoglobulin-like receptor 3DL1 precursor 2.67 CYGSFR 2 21 75 0.9 3 gi|27808666 Laminin gamma-2 chain precursor (Kalinin 2.06 CKPGVTGQR 3 44 99 0.6 3 gi|126274 Lin-12 protein precursor 0.39 SVCEK 2 20 75 3.6 2 gi|23821841 Lipin 3 (Lipin 3-like) 2.45 NGYKFLYCSAR 2 32 90 4 2 gi|1708867 Low-density lipoprotein receptor-related protein 2 precursor (Megalin) 0.38 VCGZPYGMK 2 28 90 0.5 3 gi|3915097 L-threonine 3-dehydrogenase 0.40 SGQCGKVILIP 2 24 75 2.2 4 gi|34922594 Lymphocyte antigen 75 precursor (DEC-205) 3.72 CPLVKR 2 20 75 2.1 2 gi|126730 Macrophage mannose receptor precursor (MMR) (CD206 antigen) 0.48 GCEWPLGYIZK 3 23 75 5.2 4 gi|1709131 Male-specific lethal-2 protein 3.72 CPZYK 2 21 75 2.1 2 gi|138755 Matrix protein (membrane protein) 0.17 TLWSVGCEITK 3 21 75 0.6 3 gi|2497871 Metallothionein (MT) 0.20 ZSSGCK 2 23 75 1.7 3 gi|2497895 Metallothionein-like protein type 2 MET1 & PKIWI504 0.30 MSZCGGK 2 20 75 1.3 2 gi|28201805 Methyltransferase gidB (Glucose inhibited division protein B) 2.43 IAACK 2 23 75 1.6 2 gi|24211982 Midasin (MIDAS-containing protein) 0.08 SZCSSK 2 20 75 2.4 2 gi|1706299 Mitochondrial 28S ribosomal protein S29 (S29mt) 8.76 HCAYL 2 21 75 1.2 3 gi|585955 Mitochondrial ribosomal protein S3 0.33 IGCSGR 2 20 75 0.4 4 gi|399448 Mitogen-activated protein kinase 4 (Extracellular signal-regulated kinase 4) 0.29 SCDYK 2 27 75 0.9 4 gi|1709066 Moae protein 2.99 VVVITGGGTGIGAACAR 3 31 90 2.2 2 gi|2497786 NADP-dependent malic enzyme, mitochondrial precursor (NADP-ME) 0.49 ACGALPR 2 20 75 0.3 3 gi|12643947 Nck-associated protein 1 (NAP 1) (p125Nap1) (Membrane-associated protein HEM-2) 0.40 INDIRECK 2 24 75 2.2 4 gi|128058 Negative factor (F-protein) (27 kDa protein) (3'ORF) 3.55 SCEGQK 2 20 75 1.5 2 gi|20138817 Neurogenic locus notch homolog protein 2 precursor (Notch 2) 3.65 GTCAQEK 2 22 75 4.4 4 gi|548342 Norrin (Norrie disease protein) 2.05 CSGGMR 2 28 90 4.1 2 gi|14917017 Nuclear hormone receptor family member nhr-6 (Cnr8) 2.43 MZAVCNDR 2 25 75 1.8 3 gi|1168475 Oligopeptide transport ATP-binding protein appD 2.49 CPKAMDK 2 21 75 1.6 3 gi|13631560 One cut domain family member 2 (ONECUT-2 ) (OC-2) 2.43 LAACK 2 23 75 1.6 2 gi|139279 Outer coat protein P5 2.13 TIVNIFQSCK 3 24 75 6.1 2 gi|3024340 Oxytocin receptor (OT-R) 0.04 CSSSQR 2 23 75 2 3 gi|20139193 Pannexin 0.22 LLNPSC 2 22 75 1.1 4 gi|548630 Peptide transporter PTR2 (Peptide permease PTR2) 2.43 ALAACK 2 23 75 1.6 2 gi|19860993 Period circadian protein 3 (hPER3) 2.72 CHSPFR 2 28 90 1.6 4 gi|129921 3.60 DCVGPEVEK 2 30 90 2.1 3 gi|129434 Phospholipase A2 0.22 GCFPK 2 22 75 1.1 4 gi|25091085 Phosphoribosylamine--glycine ligase (GARS) 4.23 AHANACDR 2 24 75 3.2 2 gi|548503 Phycoerythrocyanin alpha chain 0.14 SKCVR 2 20 75 3.7 3 gi|6093716 Piguamerin 4.22 TDCGGK 2 22 75 0.6 4 gi|2833397 Posttranslational flagellin modification protein 2.34 MSEILCTIZAR 2 51 99 2.8 3 gi|25008957 PR-domain protein 11 2.49 VRSGLCGG 2 20 75 1.6 2 gi|12230011 Preprotein secA subunit 0.05 DZCAK 2 23 75 7 3 gi|2492520 Probable 26S protease regulatory subunit 8.36 TDACFIR 2 21 75 1.3 2 gi|20137584 Probable ADP-ribosylation factor 0.04 DCLLLVLANK 3 43 99 1 3 gi|1171949 Probable reductase 0.05 AFCDAK 2 23 75 7 3 gi|1174862 Probable ubiquitin carboxyl-terminal hydrolase 8 (Ubiquitin thiolesterase 8) 3.95 YNQMVCLEAYRK 3 21 75 2.4 4 gi|2497367 Protein KIAA0274 0.46 CSDGVIK 2 20 75 3.1 4 gi|125419 Protein kinase 2.91 ALPICELDK 2 28 90 2.1 3 gi|3024076 Protein kinase C, zeta type (nPKC-zeta) 25.74 CHGLVPLTZRR 3 23 75 1.1 2 gi|10720183 Protein phosphatase 2C delta isoform (PP2C-delta) 7.35 VCAAIR 2 25 75 2.8 2 gi|3122889 Protein translation factor SUI1 homolog 3.65 LACGGTVK 2 22 75 4.4 4 gi|1717984 Protein U65 0.40 LILLSZPVCK 2 24 75 2.2 4 gi|1346892 PTS system, fructose-specific IIABC component (EIIABC-Fru) 2.31 KSCFDK 2 21 75 1.6 2 gi|20137585 Putative 3-methyladenine DNA glycosylase 0.33 VACSGR 2 20 75 0.4 4 gi|113825 Putative ATP-dependent RNA helicase An3 4.07 GKIGLDFCK 2 25 75 3.3 3 gi|25089927 Putative conserved oligomeric Golgi complex component 0.39 SVCEK 2 20 75 3.6 2 gi|3914150 Putative nucleolar protein K01G5.5 8.36 EYICIFK 2 32 90 1.3 3 gi|3023915 Putative RAS-related protein F43D9.2 0.47 TZLSFRFCZGR 4 22 75 1.9 3 gi|18266880 Putative serine 2.07 ILCMHGGLSQHIK 3 23 75 3.3 2 gi|140807 Putative transposase for insertion sequence element IS402 0.16 CLGSLAR 2 36 99 9.1 2 gi|2497375 Putative transposase Y4PF 0.39 ADECSK 2 20 75 3.6 2 gi|3122179 Putative uroporphyrinogen-III synthase (UROS) 2.85 DCLVAVIGPR 2 44 99 2.2 3 gi|1710020 Ras-related protein Rab-23 (Rab-15) 46.58 NPFSSCSVP 2 37 99 1.2 2 gi|20139433 Ras-related protein Rab-39A (Rab-39) 0.29 SCLLHR 2 27 75 0.9 4 gi|1718115 Replication protein E1 2.06 GACGVLSILK 3 44 99 0.6 3 gi|3287904 Rhodocetin beta subunit 0.39 ADCEEK 2 20 75 3.6 2 gi|2500670 Ribulose bisphosphate carboxylase large chain (RuBisCO large subunit) 3.86 EACKWSP 2 30 90 0.8 4 gi|2506239 RNA polymerase associated protein (ATP-dependent helicase hepA) 2.31 VLVICAK 2 21 75 1.6 2 gi|730620 RNA polymerase beta subunit (Large structural protein) (L protein) 0.07 GCPTIR 2 22 75 1 2 gi|22096020 S-adenosylmethionine:tRNA ribosyltransferase-isomerase 9.55 GGRIVCVGTTSLR 3 21 75 0.8 4 gi|8134806 S-adenosyl-methyltransferase mraW 0.04 LZSSSCK 2 23 75 2 3 gi|464732 Salivary gland SP38-40.A protein precursor 2.60 ECSGEK 2 20 75 1.1 2 gi|29336805 Selenide,water dikinase (Selenophosphate synthetase) (Selenium donor protein) 0.07 SAGCAAK 2 24 75 4.4 4 gi|8134717 Semaphorin 5B precursor (Semaphorin G) (Sema G) 0.24 SCDSPRPR 2 31 90 1.5 4 gi|25090468 Serine hydroxymethyltransferase (Serine methylase) (SHMT) 0.04 GGAILCK 2 22 75 0.7 3 gi|13124699 Serum albumin precursor (Allergen Can f 3) 3.52 TNCELFEK 2 21 75 3.8 3 gi|135079 Sexual inducer glycoprotein precursor 0.36 LCZPR 2 21 75 7.4 4 gi|20454794 SH3 domain-binding protein 5-like (Parcase protein) 2.49 QVCQDQLQTQKNR 3 22 75 2.2 2 gi|134751 SITS-binding protein (SP105) 0.29 SCIHR 2 27 75 0.9 4 gi|6226143 Smoothened homolog precursor (SMO) 0.40 KPIPDCEIK 2 24 75 2.2 4 gi|730811 Spore coat polysaccharide biosynthesis protein spsB 0.13 VLALMCQR 2 24 75 1.5 2 gi|134779 Spore coat protein SP70 precursor (Beejin protein) 0.08 SZCGESK 2 20 75 2.4 2 gi|1351099 Stage II sporulation protein 0.39 GECEK 2 20 75 3.6 2 gi|3024646 Sterol regulatory element binding protein-2 (SREBP-2) 0.16 TRCGGK 2 22 75 5.4 3 gi|25009476 Tektin B1 0.39 DACEK 2 20 75 3.6 2 gi|136171 Thrombomodulin precursor (Fetomodulin) (TM) 0.36 CLZPR 2 21 75 7.4 4 gi|135077 Transcriptional factor SWI5 2.24 AYACPZGK 2 25 75 2.1 3 gi|119550 Transcriptional regulator ERG (Transforming protein ERG) 3.68 NSPDECSVAKGGK 3 25 75 1.9 2 gi|30172878 Transcriptional repressor CTCFL (CCCTC-binding factor) 3.65 CGSGEAK 2 22 75 4.4 4 gi|2498629 Transcriptional repressor NF-X1 (Nuclear transcription factor, X box-binding, 1) 0.40 TCEZGRTR 2 37 99 3 2 gi|1174638 Transitional endoplasmic reticulum ATPase 5.16 GVLFYGPPGCGK 2 43 99 1.8 4 gi|464834 Tremerogen A-I 0.03 DPGASSGGC 2 22 75 1.1 2 gi|38258718 tRNA pseudouridine synthase A 0.43 TLPAAGCZ 2 29 90 6.2 3 gi|3023518 Tubulin-specific chaperone B (Tubulin folding B) 2.13 SLTIAEFKCK 3 24 75 6.1 2 gi|1351248 Tyrosine-protein kinase receptor Tie-1 precursor 0.29 SCLHR 2 27 75 0.9 4 gi|119687 UDP-glucose 4-epimerase (Galactowaldenase) 0.14 DGTCVR 2 20 75 3.7 3 gi|549157 UDP-glucuronosyltransferase 2B12 precursor, microsomal (UDPGT) 0.02 SGNCGK 2 28 90 4 2 gi|2497487 UMP-CMP kinase () (Deoxycytidylate kinase) 2.43 GTQCAR 2 23 75 1.6 3 gi|33516968 UPF0082 protein (PRO0477) 2.49 GCGAAPGR 2 26 75 1.6 4 gi|418177 Vacuolar ATP synthase catalytic subunit A (V-ATPase A subunit) 0.16 CIGSPSR 2 36 99 9.1 2 gi|131092 Vitamin K-dependent protein Z precursor 0.29 CSLLHR 2 27 75 0.9 4 gi|33301872 V-type ATP synthase beta chain (V-type ATPase subunit B) 0.29 SCLHR 2 27 75 0.9 4 gi|139701 Wnt-10 protein 6.29 SGSCQLK 2 26 75 1.4 4 gi|3123031 Wnt-2b protein precursor (XWnt-2b) 2.45 GTDGZEVMCZGR 2 32 90 4 3 gi|139800 Xanthine dehydrogenase (XD) (Rosy locus protein) 4.02 MIQCAAR 2 22 75 2.7 4 gi|586428 Yippee-like protein YBL049W 4.19 NIZKCT 2 20 75 0.6 2 gi|1176560 YME1 protein homolog 2.49 TCZVSNR 2 23 75 1.6 2 gi|12585545 Zinc finger protein 217 0.43 ECSYZGK 2 30 90 7.4 4 gi|34925618 Zinc finger protein 429 0.10 GYKTVGDCK 3 25 75 7.6 3

Functional unknown proteins: gi|1175068 Hypothetical 25.3 kDa protein IN 39K-P43 intergenic region (ORF7) 0.05 DZCDAK 2 23 75 7 3 gi|731617 Hypothetical 17.6 kDa protein in CBP2 5'region 16.86 HFFFCGHK 2 31 90 1 4 gi|140187 Hypothetical 18.6 kDa protein in alpha-glucosidase 3'region (ORF2) 3.65 CHAADK 2 22 75 4.4 4 gi|140773 Hypothetical 18.6 kDa protein in HISH-HISA intergenic region (ORF1) 2.22 CHGLAR 2 20 75 1.9 2 gi|2497015 Hypothetical 41.0 kDa protein T23F11.3 in chromosome III 2.70 HCSSSE 2 23 75 0.9 4 gi|2493219 Hypothetical 42.5 kDa protein (ORF58) 0.05 MSCAK 2 23 75 7 3 gi|731753 Hypothetical 90.1 kDa protein in OYE2-GND1 intergenic region 0.21 ALESSNMMFQQKCEK 3 24 75 3 2 gi|1730631 Hypothetical protein B0361.9 in chromosome III precursor 0.49 CAEKPR 2 20 75 0.3 3 gi|1723518 Hypothetical protein C22E12.04 in chromosome 0.08 SZCSSK 2 20 75 2.4 2 gi|6226929 Hypothetical protein C38C10.5 in chromosome III 0.08 ECLGDAPAQR 3 41 99 0.6 2 gi|20140418 Hypothetical protein C3G6.03c in chromosome 0.29 CGEGSDK 2 25 75 0.9 4 gi|25091647 Hypothetical protein CG12467 in chromosome 2.24 YAAYCER 2 25 75 2.1 3 gi|465798 Hypothetical protein F44E2.4 in chromosome III 0.41 DIVVAKCGESPIK 3 21 75 2 3 gi|1176068 Hypothetical protein HI1671 0.36 ICZPR 2 21 75 7.4 4 gi|2496400 Hypothetical protein MG350 homolog (G12_orf328b) 0.05 MSCAK 2 23 75 7 3 gi|2833538 Hypothetical protein MJ0694 2.43 ALACK 2 23 75 1.6 2 gi|28380221 Hypothetical protein PYUK71.03c in chromosome 0.11 DDHLGSCVIDZK 3 26 75 1.3 4 gi|6647919 Hypothetical protein RP277 2.49 ZHZEIC 2 23 75 1.6 4 gi|586856 Hypothetical protein yaaC 0.49 ACLITR 2 20 75 0.3 3 gi|2495502 Hypothetical protein yagW 0.34 SGLSCK 2 20 75 6.1 4 gi|2501612 Hypothetical protein YPL207W 0.08 GGGZCSSK 2 20 75 2.4 2 gi|466187 Hypothetical protein ypuI (ORFX9) 0.08 CERQIHEGK 3 41 99 0.6 2 gi|21431852 Hypothetical protein ZK643.6 in chromosome III 0.11 CPATZGK 2 22 75 0.6 2 gi|24418809 Putative HTH-type transcriptional regulatory protein PF1851 0.12 GGCFDLVATR 3 38 99 0.9 2 * H: sheared; L: control Table C. Proteins alterations after 6 hours of shear stress

Accesion # Protein Name H:L* Matched Sequence Charge Score Confidence % Error Peptide Number gi|6226066 30S ribosomal protein S14 2.11 LCFRHLAYNGSLPGVK 3 27 75 1.1 3 gi|21263399 3-dehydroquinate synthase 3.91 AGLPVCGPK 2 20 75 0.4 3 gi|133820 40S ribosomal protein S17 0.41 VCEEIAIIPSKK 3 35 99 1 2 gi|417718 40S ribosomal protein S37 (CEP76) (YS24) 0.28 CHSVYK 2 21 75 4.1 3 gi|3334110 6-phosphogluconate dehydrogenase, decarboxylating 0.11 CLSAMK 2 22 75 1 4 gi|543845 (NAG kinase) (AGK) 10.02 CGGSVIR 2 31 90 2.6 4 gi|29839752 ADAM 10 precursor (A disintegrin and metalloproteinase domain 10) 0.14 CTLKPGK 2 22 75 2.3 2 gi|14423637 ADAM 29 precursor (A disintegrin and metalloproteinase domain 29) 3.10 SCHDR 2 28 90 5.7 2 gi|117788 Adenylate cyclase, type IV (ATP pyrophosphate-lyase) (Adenylyl cyclase) 0.14 CVQKGPK 2 22 75 2.3 2 gi|2500963 Alanyl-tRNA synthetase (Alanine--tRNA ligase) (AlaRS) 0.50 HLTCFTMGGHHAFNR 3 26 75 5 4 gi|8927986 Alkyldihydroxyacetonephosphate synthase (Alkyl-DHAP synthase) 0.21 GIHPCTMR 2 34 90 2.3 3 gi|24636860 Aminomethyltransferase (Glycine cleavage system T protein) 0.33 SLYDAGVIPCGLGAR 3 21 75 0.3 2 gi|730947 Angiopoietin 1 receptor precursor (Tyrosine-protein kinase receptor TIE-2) 0.34 CSGPEGZK 2 23 75 12 4 gi|38604884 Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) 0.36 ILVALCGR 2 26 75 0.4 2 gi|37999913 Anti-epilepsy peptide precursor 0.15 GSNGCK 2 26 75 3.3 2 gi|1170471 Apoptosis inhibitor 3 (IAP-3) 0.30 CAAGVTTZPVZR 3 46 99 0.4 3 gi|6225170 ATP-dependent Clp protease ATP-binding subunit clpX 4.68 KELICSFZSK 3 46 99 5.4 4 gi|1705813 Basic endochitinase precursor 0.28 NEGSCPGK 2 24 75 1.9 2 gi|3023391 Beta-defensin 2 precursor (BD-2) (sBD2) 5.45 CPGTMR 2 22 75 9.5 2 gi|11131432 Biotin synthase (Biotin synthetase) 0.11 CEYIAKLAK 3 25 75 0.8 4 gi|124021 Bowman-Birk type trypsin inhibitor TI1 0.34 CSDAZK 2 23 75 12 4 gi|728984 Breast cancer type 1 susceptibility protein 18.65 FCMLKLLNQK 3 20 75 7.1 4 gi|22653670 Bromodomain adjacent to zinc finger domain protein 1B 0.34 CSZGSYR 2 23 75 12 4 gi|28376972 Calpain 5 (nCL-3) (htra-3) 3.09 QNRGGGCINHK 3 21 75 3 2 gi|32129434 Cathepsin B-like CP2 precursor (Cathepsin B-like protease B2) 0.21 CADGSSK 2 23 75 7.5 2 gi|26391975 CENP-B homolog protein 2 (CBHP-2) 2.42 CLKHGLK 2 31 90 0.5 4 gi|3182957 cGMP-inhibited 3',5'-cyclic phosphodiesterase B 0.34 CSPFZR 2 23 75 12 4 gi|1350651 Chloroplast 50S ribosomal protein L4 4.80 EIYCG 2 22 75 2.4 2 gi|116935 Core antigen 0.25 SQSPASNC 2 35 99 9.5 2 gi|1706413 Corticosteroid 11-beta-dehydrogenase, isozyme 2 (11-DH2) 0.42 VSIILPACFK 3 31 90 2.1 2 gi|1705992 Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) 0.34 SCYSR 2 23 75 12 4 gi|3913389 Cystatin precursor 7.37 GGVEKVCSVHK 3 30 90 0.5 2 gi|118155 Cysteine proteinase precursor 7.41 CSVPKAK 2 24 75 1.3 2 gi|20137742 D-arabinitol 4-dehydrogenase 6.69 GAGPLTLQSCDNLR 3 25 75 1 4 gi|30172942 Death associated transcription factor 10.02 CGAQAGIK 2 31 90 2.6 4 gi|1169354 Delta-like protein precursor (DLK) (Preadipocyte factor 1) (Pref-1) 3.34 CPAGFVDK 2 20 75 4.5 2 gi|729314 Deoxyribose-phosphate aldolase (Phosphodeoxyriboaldolase) 0.33 EACAAANVLLK 2 23 75 0.5 2 gi|39932422 Depressant scorpion toxin BmKIM precursor 0.15 GSNGCK 2 26 75 3.3 2 gi|12643849 DNA mismatch repair protein MSH6-2 (AtMsh6-2) (MutS homolog 7) 0.25 DCSGER 2 27 75 9.5 2 gi|131813 DNA repair protein RAD4 0.43 ECGYLK 2 21 75 9.4 3 gi|6094451 DNA terminal protein (Bellett protein) (pTP protein) 18.65 NVSSVCFLQSAR 3 20 75 7.1 4 gi|18266792 DNA topoisomerase I (Omega-protein) (Relaxing enzyme) (Untwisting enzyme) 0.37 CGGDLIVKYNEK 3 20 75 2.5 3 gi|729352 DNA43 protein 4.68 CGSPINISLHK 3 46 99 5.4 4 gi|3914818 DNA-directed RNA polymerase I largest subunit 4.02 CMDPZGTZLK 3 33 90 5.5 3 gi|20141240 Dual specificity protein kinase CLK3 (CDC like kinase 3) 0.08 YVKENCKPLK 3 24 75 0.6 4 gi|1352338 Ectatomin subunit B (EA) 22.78 KCEGSIATMIK 3 25 75 6.4 3 gi|17368882 Electron transport complex protein rnfE (Nitrogen fixation protein rnfE) 7.41 CSPRPR 2 24 75 1.3 2 gi|12229784 Ellis-van Creveld syndrome protein homolog 18.65 KKPDDELCQK 3 20 75 7.1 4 gi|11386722 Enamelin precursor 4.88 STPCSVK 2 22 75 3.1 2 gi|1352340 Eosinophil cationic protein precursor (ECP) (Ribonuclease 3) (RNase 3) 2.11 IRCPR 2 26 75 6.6 3 gi|2827756 Ephrin type-A receptor 1 precursor (Tyrosine-protein kinase receptor EPH) 0.30 RGLYLAFHNPGACVALVSVR 3 22 75 1.5 3 gi|232057 Epidermin biosynthesis protein epiB 0.12 YWDGCD 2 21 75 6 2 gi|13959369 Eppin precursor (Epididymal protease inhibitor) 0.48 EEZEHQERDLCTR 3 20 75 2.4 4 gi|7387904 F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) 0.06 GCFIEK 2 22 75 1.5 3 gi|2498379 Ferrous iron transport protein B homolog 0.20 YGTGCSR 2 20 75 0.3 3 gi|3913647 Fibrillin 2 precursor 0.12 CHAGFQR 2 26 75 6 3 gi|232109 FL cytokine receptor precursor (Tyrosine-protein kinase receptor flk-2) 0.03 ADSCEK 2 20 75 1.4 2 gi|120554 Follitropin beta chain precursor (Follicle-stimulating hormone beta subunit) 0.33 SIQLCILLWZLR 3 21 75 0.3 2 gi|21362543 Formamidopyrimidine-DNA glycosylase (Fapy-DNA glycosylase) 0.11 QCGHPIEIAK 3 25 75 0.8 4 gi|544354 F-spondin precursor 0.19 FCGGGIQER 3 25 75 0.5 3 gi|584910 G2/mitotic-specific cyclin-B 7.81 CSKAGGVDGHK 2 22 75 0.8 3 gi|6016095 Galanin receptor type 2 (GAL2-R) (GALR2) 7.41 TLDPAC 2 24 75 1.3 2 gi|464431 Genome polyprotein 3.21 CKGASSTR 2 23 75 0.8 3 gi|130409 Genome polyprotein [Contains: Coat protein VP4 (P1A); Coat protein VP2 (P1B); Coat protein VP3 (P1C) 0.09 SGIYYCKSTAK 3 20 75 4.2 3 gi|121398 Glp-1 protein precursor 0.02 CPAHIR 2 31 90 1.3 2 gi|33301370 Glucans biosynthesis glucosyltransferase 3.21 ACGGAFR 2 23 75 0.8 3 gi|30173147 Glutamyl-tRNA synthetase (Glutamate--tRNA ligase) (GluRS) 0.31 NTFFCTIK 2 31 90 0.5 4 gi|27151503 GTP cyclohydrolase III 10.44 SCLGYGK 2 25 75 2.1 3 gi|462324 Heat shock 70 kDa protein 11.79 VCNPIITK 2 37 99 1.3 2 gi|123644 Heat shock cognate 71 kDa protein 11.79 VCNPIITK 2 37 99 1.3 2 gi|122887 Hemagglutinin precursor [Contains: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain] 0.27 IAVGDCPR 2 24 75 0.7 4 gi|6226894 Heterogenous nuclear ribonucleoprotein U (hnRNP U) 7.41 VCFEMK 2 24 75 1.3 2 gi|34395705 HIPL2 protein precursor 0.12 SZCNSK 2 20 75 4.4 4 gi|1730880 Homeobox protein YOX1 0.19 CPAPSK 2 26 75 2.1 4 gi|3025116 HTH-type transcriptional regulator abgR 0.43 ECGYLQS 2 21 75 9.4 3 gi|27923788 Inhibin beta chain precursor (Activin beta chain) 0.09 SNNLCRVLZK 3 20 75 4.2 3 gi|29427597 Inorganic pyrophosphatase (Pyrophosphate phospho-hydrolase) (PPase) 0.03 IILSACEK 2 20 75 1.7 3 gi|14285770 Insect toxin 5 (AaH IT5) (AaHIT5) (AaIT5) 3.75 SETNTCD 2 22 75 0.4 4 gi|9296994 Kallikrein 5 precursor (Stratum corneum tryptic enzyme) 0.07 CLVSGWGTTKSPQVHFPK 3 24 75 2.1 3 gi|17865497 Laminin gamma-3 chain precursor (Laminin 12 gamma 3) 0.07 CNGHASEZGPDVAGQLAZR 3 24 75 2.1 3 gi|1170755 Late expression factor 4.80 LZGMSGC 2 22 75 2.4 2 gi|37537904 Leukocyte immunoglobulin-like receptor subfamily B member 5 precursor 0.16 CYYYYR 2 32 90 0.7 3 gi|585398 Limulus clotting factor C precursor (FC) 0.33 VQPICLPTDITTR 3 21 75 0.3 2 gi|126274 Lin-12 protein precursor 0.47 CGADEK 2 23 75 6.6 2 gi|1170790 Lipase B precursor (CALB) 0.34 TCSGIVTP 2 25 75 12 4 gi|29427582 LOB domain protein 31 2.26 MSGSTTGZGGPCGACK 4 21 75 2.5 4 gi|1708888 Lysine biosynthesis regulatory protein lys 7.37 QCVYVLNPK 3 30 90 0.5 2 gi|38257899 LysM-domain GPI-anchored protein 2 precursor 0.13 ACSSSVRK 2 20 75 0.5 3 gi|37537754 Lysophosphatidylcholine receptor G2A (G2 accumulation protein) 0.16 LIEESC 2 20 75 2 2 gi|28380114 Major pollen allergen Pla l 2.02 AKTDAPGC 2 21 75 0.4 3 gi|24638048 Mas-related G protein-coupled receptor MRGF (Mas-related gene F protein) 4.02 MCPGMSEAR 3 33 90 5.5 3 gi|2495077 Metabotropic glutamate receptor 4 precursor (mGluR4) 2.11 VGLCPR 2 26 75 6.6 3 gi|127413 Metallothionein 0.49 SZAGSCK 2 22 75 0.6 2 gi|1346594 Metallothionein-IV (MT-IV) 0.08 GGSDKZSZCP 2 28 90 0.9 4 gi|2507587 Metallothionein-like protein 2A & 2B 41.32 CDPZTZK 2 29 90 1.5 3 gi|136545 Muscarinic toxin 2 precursor 14.76 CZGTDK 2 21 75 2 2 gi|113352 NADPH-dependent butanol dehydrogenase (BDH) 0.14 AIGDACTGSNPR 3 20 75 0.5 2 gi|2506355 NADP-specific glutamate dehydrogenase 1 (NADP-GDH 1) 0.01 RIMINZFNECIDYAK 4 21 75 1.6 2 gi|34922569 Netrin G1 precursor (Laminet-1) 2.11 CKZNLHATSZLYDNSK 4 24 75 1.1 4 gi|14423770 Olfactory receptor 10H3 0.42 LACGSK 2 22 75 2 4 gi|32699583 Ornithine carbamoyltransferase, catabolic (OTCase) 0.33 SFWPDAALVAQCR 3 21 75 0.3 2 gi|1175429 Paired amphipathic helix protein pst1 (SIN3 homolog 1) 0.34 SCGPSYR 2 23 75 12 4 gi|131104 Parvalbumin alpha 18.65 CFSDGARVLNDK 3 20 75 7.1 4 gi|39931671 Peptide chain release factor 3 (RF-3) 3.21 ICSGEFR 2 23 75 0.8 3 gi|13626145 Peroxidase 0.02 CPMGHGR 2 31 90 1.3 2 gi|26398007 Peroxidase E5 2.11 RLCPR 2 26 75 6.6 3 gi|1709682 Peroxisomal alkyl hydroperoxide reductase (Thioredoxin peroxidase type II) 0.09 FASDPGCAFTK 3 22 75 2 4 gi|1709595 Pheromone-binding protein-related protein 2 precursor 0.18 DHLLELANECK 3 20 75 0.7 3 gi|30172998 Phosphoglycerate kinase 0.34 ALSCPVR 2 31 90 0.4 2 gi|129397 Phospholipase A2 isozyme 0.06 GCFPK 2 22 75 1.5 3 gi|25108915 Phospholipase A2 precursor (Phosphatidylcholine 2-acylhydrolase) 0.16 EEPEPC 2 20 75 2 2 gi|30173076 PII uridylyl-transferase 2.11 RLCPR 2 26 75 6.6 3 gi|7388004 Polygalacturonase precursor (PG) 0.12 NAPSGTC 2 26 75 6 3 gi|136232 Potassium transport protein, low-affinity 10.53 RAPHCSLK 2 27 75 3.7 3 gi|2499826 Pregnancy-associated glycoprotein 2 precursor (PAG 2) 2.11 VIGCPR 2 26 75 6.6 3 gi|548590 Pre-mRNA splicing factor RNA helicase PRP16 0.43 FEDVTDSECTK 3 25 75 0.5 3 gi|130804 Pre-mRNA splicing factor RNA helicase PRP2 0.34 DCLVIPK 2 23 75 12 3 gi|12643627 Preprotein translocase secY subunit, chloroplast precursor (CpSecY) 0.33 MVTATTTPPQCWR 3 21 75 0.3 2 gi|1731349 Probable helicase helY 0.13 ACSALER 2 20 75 0.5 3 gi|23396730 Probable molybdenum cofactor biosynthesis protein 0.23 CNTAVAAK 2 28 90 5.9 4 gi|24638455 Probable thiamine biosynthesis protein thiC 2.11 QAKEGVDFMTLHCGITK 3 27 75 1.1 3 gi|1172736 PTS system, N-acetylgalactosamine-specific IIB component 2 3.09 QKILLVCK 2 26 75 0.7 2 gi|18202248 Putative ankyrin-repeat protein FPV031 0.30 LDYSTCMSNK 3 51 99 0.4 4 gi|2493776 Putative cuticle collagen C09G5.3 0.02 CPPGPR 2 31 90 1.3 2 gi|2497556 Putative molluscan insulin-related peptide(S) receptor precursor 0.08 QSLTPCGGGQFK 3 23 75 0.6 4 gi|15214341 Putative nucleic acid binding protein At4g18375 0.27 VITIYCSVKEK 3 20 75 0.7 3 gi|2498688 Putative odorant-binding protein A10 precursor 0.41 CLEGTGPZTPDAK 2 56 99 6.3 3 gi|3914148 Pyruvate-flavodoxin 0.37 CVMVZPHAALRVK 3 20 75 2.5 3 gi|3024529 Ras-related protein Rab11E 0.20 YRCZSN 2 20 75 0.3 3 gi|115131 Regulatory protein brlA (Bristle A protein) 0.48 EPGCNGR 2 21 75 1.5 2 gi|1352838 Replication protein E1 22.78 QCNZLQTSRK 3 25 75 6.4 3 gi|2500656 Ribulose bisphosphate carboxylase large chain precursor 2.06 EACKWSP 2 26 75 0.3 4 gi|133312 RNA polymerase sigma factor RPOD (SIGMA-80) 0.19 YDCSMK 2 34 90 3.5 2 gi|32129843 RNA-binding protein PIPPin 41.32 ICPIPPK 2 29 90 1.5 3 gi|29840871 Semaphorin 4A precursor (Semaphorin B) (Sema B) 0.06 SECAFK 2 20 75 1.4 3 gi|730843 Shuttle craft protein 2.74 SZGCGR 2 26 75 0.5 4 gi|20532375 Shwachman-Bodian-Diamond syndrome protein homolog 0.18 CVNPETK 2 20 75 9.9 2 gi|29611858 Sodium bicarbonate transporter-like protein 11 0.09 CKDFVPFGK 3 22 75 2 4 gi|123704 Sperm histone P2B (ST2B) 7.41 CSPRR 2 24 75 1.3 2 gi|21362964 Steroidogenic acute regulatory protein (StAR) (StARD1) 4.02 MASSSTALSLC 3 33 90 5.5 3 gi|267108 Tetranectin precursor (TN) (Plasminogen-kringle 4 binding protein) 0.33 TFHEASEDCISR 3 21 75 0.3 2 gi|37999906 THO complex subunit 1 (Tho1) (Nuclear matrix protein p84) 0.35 NPVQCYEK 3 40 99 6.2 4 gi|1172018 Topoisomerase IV subunit 0.30 IAFENGSKVEELEIIGTCGR 3 22 75 1.5 3 gi|7531133 Transcription elongation factor greA (Transcript cleavage factor greA) 0.10 DLVFTDKVGVGCK 2 26 75 3.1 2 gi|586313 Transcription factor SMP1 0.30 CGSTYVNNK 3 46 99 0.4 3 gi|13431922 Transforming acidic coiled-coil-containing protein 0.34 LASTSCGQK 2 31 90 0.4 2 gi|464834 Tremerogen A-I 5.61 DPGASSGGC 2 20 75 5.4 2 gi|2498562 tRNA delta(2)-isopentenylpyrophosphate transferase (IPP transferase) 6.69 VPPLIVICGTTASGK 3 25 75 1 4 gi|125006 Trypsin inhibitor 2.11 RICPR 2 26 75 6.6 3 gi|39932073 Tryptophanyl-tRNA synthetase (Tryptophan--tRNA ligase) (TrpRS) 12.56 CHAFK 2 22 75 2.2 2 gi|135409 Tubulin alpha-2 chain 41.32 CDPLHGK 2 29 90 1.5 3 gi|1174826 Tyrosine-protein kinase TXK (PTK-RL-18) (Resting lymphocyte kinase) 0.34 SCYIHR 2 23 75 12 4 gi|731045 Ubiquitin carboxyl-terminal hydrolase 12 (ubiquitin thiolesterase 12) 0.32 EGDKVCIVPK 3 23 75 0.8 3 gi|1717852 Ubiquitin-activating enzyme E1-like (polymerase-interacting protein 2) 41.32 NCPVZSK 2 29 90 1.5 3 gi|549157 UDP-glucuronosyltransferase 2B12 precursor, microsomal (UDPGT) 0.15 SGNCGK 2 26 75 3.3 2 gi|131826 V(D)J recombination activating protein 1 (RAG-1) 0.20 SSCPAK 2 21 75 4.1 4 gi|139701 Wnt-10 protein 0.43 SGSCQLK 2 23 75 5.3 3 gi|1176560 YME1 protein homolog 0.18 TCZVSNR 2 20 75 9.9 2 gi|20141013 Zinc finger imprinted 3.62 KSYQCNEZEK 3 31 90 1.2 4 gi|12230861 Zinc finger protein 219 41.32 DCPFZGK 2 29 90 1.5 3 gi|11136122 Zinc finger protein 223 0.04 CRSALTVHZK 3 56 99 1.1 3 gi|12643896 Zinc finger protein 236 0.02 CPQZFR 2 31 90 1.3 2 gi|20141029 Zinc finger protein 341 5.85 CAGZAKGFSR 3 34 90 3 2 gi|466206 Zona pellucida sperm-binding protein 2 precursor 0.34 CSYSR 2 23 75 12 4 gi|13634073 Zonadhesin precursor 2.01 ISLQCPAHSK 3 37 99 4.7 3

Functional unknown proteins: gi|2495215 Hypothetical 20.9 kDa protein in ROX1-SPE3 intergenic region 0.33 SSZGCGSSFDIEN 3 21 75 0.3 2 gi|1353036 Hypothetical 21.6 kDa protein in ATP12-RPL17B intergenic region 0.12 GPSGCLK 2 24 75 6 2 gi|141469 Hypothetical 22 kDa protein in TRPE 5'region 0.43 ZDGCRIWEK 2 20 75 0.6 2 gi|1176588 Hypothetical 23.5 kDa protein in RFA2-STB1 intergenic region 4.68 GTVLISCPHZK 3 46 99 5.4 4 gi|2497152 Hypothetical 52.4 kDa protein in ILV2-ADE17 intergenic region 5.37 GCVGTSYK 2 24 75 2.3 3 gi|141330 Hypothetical 7.6 kDa protein in TK 5'region (Q1 ORF) 3.75 KYDZCL 2 22 75 0.4 4 gi|549667 Hypothetical 87.9 kDa protein in PTM-IRX1 intergenic region precursor 0.18 LQCPVZR 2 20 75 9.9 2 gi|136824 Hypothetical gene 48 protein 0.43 STCPAPR 2 20 75 5.3 4 gi|1723105 Hypothetical protein 3.20 YICFGKK 2 39 99 5.9 2 gi|465775 Hypothetical protein C07A9.9 in chromosome III 0.02 CPQZFR 2 31 90 1.3 2 gi|2499163 Hypothetical protein in napC 3'region 0.47 GCSPASER 2 23 75 6.6 2 gi|2494448 Hypothetical protein MJ0208 0.08 ZINVCPNGAIVK 3 23 75 0.6 4 gi|2496118 Hypothetical protein MJ0751 0.32 TSKLCPIZGZK 3 23 75 0.8 3 gi|32699836 Hypothetical protein MJ1262 0.17 LEDNCGVVGLTSFNK 3 24 75 0.6 2 gi|2496206 Hypothetical protein MJECS12 0.43 EFZGNCSKIK 2 20 75 0.6 2 gi|11135697 Hypothetical protein MPN110 (C09_orf718) 0.49 EICYVYDFNMYR 3 26 75 2.7 3 gi|6647919 Hypothetical protein RP277 0.25 ZHZEIC 2 35 99 9.5 2 gi|2829590 Hypothetical protein Rv2635 0.04 RCSAVDHSSR 3 56 99 1.1 3 gi|13878889 Hypothetical protein TC0746 precursor 0.49 IRFFSPPEICIMR 3 26 75 2.7 2 gi|1177008 Hypothetical protein yxiL 2.22 DSVIMCMTKK 3 23 75 0.9 2 gi|12644491 Probable 50S ribosomal protein L25 0.47 VVCKPK 2 21 75 2.3 2 * H: sheared; L: control