Supporting Information for Proteomics DOI 10.1002/Pmic.200400942

Supporting Information for Proteomics DOI 10.1002/pmic.200400942

Wei-Jun Qian, Jon M. Jacobs, David G. Camp II, Matthew E. Monroe, Ronald J. Moore, Marina A. Gritsenko, Steve E. Calvano, Stephen F. Lowry, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Ronald G. Tompkins and Richard D. Smith

Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry

ã 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Supplemental Table 1: List of 804 identified plasma proteins. Note: Reference IDs correspond to either SwissProt, NCBI, or PIR database entries. For each protein, one representive peptide sequence and the peptide charge_state, SEQUEST Xcorr, and Delcn are listed. The number of different peptides identifying each specific protein is also indicated. To facilitate comparison of protein abundances between the untreated and treated samples, the numbers of peptide hit, the protein abundance ratio (treated/untreated) calculated from peptide peak area ratios, and the standard deviation of peptide peak area ratios for each protein are also listed. No abundance ratio is shown if the protein has no common peptide identified in the two samples. Whether the same protein ID was reported in reference 16 and reference 27 (195 proteins observed from two different sources) is also indicated.

Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:ALBU_HUMAN serum albumin precursor 360 K.EFNAETFTFHADICTLSEK.E 1 6.942 1

7858 7141 1.23 0.29 YES YES

SW:CO3_HUMAN complement c3 precursor 224 R.IFTVNHK.L 1 6.929 0.597 [contains: c3a anaphylatoxin] 916 848 0.91 0.19 YES YES

SW:APB_HUMAN apolipoprotein b-100 precursor 219 K.KLTISEQNIQR.A 1 6.975 1 (apo b-100) [contains: 574 525 1.03 0.44 YES YES

SW:A2MG_HUMAN alpha-2-macroglobulin precursor 211 K.KDNSVHWERPQKPK.A 1 5.715 0.526 (alpha-2-m) 1030 959 1.09 0.24 YES YES

SW:CO4_HUMAN complement c4 precursor 160 R.NVNFQK.A 1 7.054 0.574 [contains: c4a anaphylatoxin] 532 492 1.06 0.36 YES YES

SW:TRFE_HUMAN serotransferrin precursor 150 R.AIAANEADAVTLDAGLVYDAYLAPNN 3 7.436 0.563 (siderophilin) (beta-1-metal 979 998 1.14 0.42 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:FINC_HUMAN fibronectin precursor (fn) (cold- 100 R.TKTETITGFQVDAVPANGQTPIQR.T 1 5.206 0.517 insoluble globulin) (cig) 328 343 1.17 0.45 YES YES

SW:A1AT_HUMAN alpha-1-antitrypsin precursor 92 K.LSITGTYDLK.S 1 6.618 0.617 (alpha-1 protease inhibitor) 504 516 1.11 0.46 YES YES

SW:CERU_HUMAN ceruloplasmin precursor (ec 1 89 R.SVPPSASHVAPTETFTYEWTVPK.E 1 6.884 0.58

275 307 1.05 0.38 YES YES

SW:FIBA_HUMAN fibrinogen alpha/alpha-e chain 83 R.GDFSSANNR.D 1 6.430 0.583 precursor 285 325 1.34 0.37 YES YES

SW:FIBG_HUMAN fibrinogen gamma chain 81 K.FFTSHNGMQFSTWDNDNDKFEGN 1 5.993 0.616 precursor 277 276 1.17 0.51 YES

SW:FIBB_HUMAN fibrinogen beta chain precursor 81 R.TPCTVSCNIPVVSGK.E 1 6.520 0.565

327 345 1.23 0.43 YES YES

SW:VTDB_HUMAN vitamin d-binding protein 68 R.VCSQYAAYGEK.K 1 5.895 0.587 precursor (dbp) (group-specific 188 180 1.28 0.4 YES YES

SW:CFAH_HUMAN complement factor h precursor (h 65 K.SPPEISHGVVAHMSDSYQYGEEVTY 1 6.001 0.578 factor 1) 168 166 1.29 0.38 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:APA1_HUMAN apolipoprotein a-i precursor (apo- 63 R.AHVDALR.T 1 3.407 0.429 ai) 282 269 1.12 0.43 YES YES

SW:PLMN_HUMAN plasminogen precursor (ec 3 57 K.LSSPAVITDK.V 1 6.902 0.537

106 107 1.19 0.44 YES YES

SW:HPTR_HUMAN haptoglobin-related protein 57 K.KQLVEIEK.V 1 5.728 1 precursor 222 216 1.27 0.48 YES

SW:HEMO_HUMAN hemopexin precursor (beta-1b- 54 R.GECQAEGVLFFQGDR.E 1 4.730 0.419 glycoprotein) 169 161 1.23 0.33 YES YES

SW:ITH4_HUMAN inter-alpha-trypsin inhibitor heavy 53 K.VRPQQLVK.H 1 5.178 0.526 chain h4 precursor 147 127 1.14 0.59 YES YES

SW:CFAB_HUMAN complement factor b precursor 53 R.DLLYIGK.D 1 6.242 0.676 (ec 3 127 127 1.12 0.33 YES YES

SW:HPT2_HUMAN haptoglobin-2 precursor 52 K.DYAEVGR.V 1 6.203 0.564

337 301 1.64 0.41 YES YES

SW:CO5_HUMAN complement c5 precursor 46 K.TLLPVSKPEIR.S 1 5.604 0.525 [contains: c5a anaphylatoxin] 134 107 0.88 0.37 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:ITH2_HUMAN inter-alpha-trypsin inhibitor heavy 41 K.TQVADAK.R 1 2.081 0.302 chain h2 precursor 146 133 0.94 0.33 YES YES

SW:C4BP_HUMAN c4b-binding protein alpha chain 40 R.GSSVIHCDADSK.W 1 7.339 0.589 precursor (c4bp) (proline-rich 94 90 1.35 0.48 YES YES

SW:A2HS_HUMAN alpha-2-hs-glycoprotein 39 K.AALAAFNAQNNGSNFQLEEISR.A 1 4.231 0.513 precursor (fetuin-a) (alpha-2-z- 155 150 1.18 0.47 YES YES

SW:KNG_HUMAN kininogen precursor (alpha-2-thiol 38 K.KYNSQNQSNNQFVLYR.I 1 5.150 0.572 proteinase inhibitor) [contains: 86 83 0.9 0.32 YES YES

SW:A1AH_HUMAN alpha-1-acid glycoprotein 2 38 K.SDVVYTDWK.K 1 5.890 0.565 precursor (agp 2) (orosomucoid 2) 163 150 0.95 0.45 YES

SW:TTHY_HUMAN transthyretin precursor 37 R.GSPAINVAVHVFR.K 1 5.968 0.52 (prealbumin) (tbpa) (ttr) (attr) 199 190 1.33 0.33 YES YES

SW:ITH1_HUMAN inter-alpha-trypsin inhibitor heavy 36 K.QLVHHFEIDVDIFEPQGISK.L 1 6.657 0.536 chain h1 precursor 120 108 1 0.34 YES YES

SW:VTNC_HUMAN vitronectin precursor (serum 36 K.PFDAFTDLK.N 1 4.306 0.482 spreading factor) (s-protein) 61 57 0.98 0.28 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:A1BG_HUMAN alpha-1b-glycoprotein 34 R.LETPDFQLFK.N 1 5.732 0.531

126 112 1.19 0.53 YES YES

SW:THRB_HUMAN prothrombin precursor (ec 3 34 K.GQPSVLQVVNLPIVER.P 1 6.745 0.595

64 75 1.42 0.32 YES YES

SW:GELS_HUMAN gelsolin precursor, plasma (actin- 33 K.FDLVPVPTNLYGDFFTGDAYVILK.T 2 4.156 0.543 depolymerizing factor) (adf) 127 126 0.96 0.33 YES YES

SW:APOH_HUMAN beta-2-glycoprotein i precursor 32 K.ATVVYQGER.V 1 5.582 0.514 (apolipoprotein h) (apo-h) (b2gpi) 80 71 1.36 0.4 YES YES

SW:HRG_HUMAN histidine-rich glycoprotein 29 K.NLVINCEVFDPQEHENINGVPPHLGH 1 6.094 0.512 precursor (histidine-proline rich 82 85 1.03 0.42 YES YES

SW:ANT3_HUMAN antithrombin-iii precursor (atiii) 28 K.ANRPFLVFIR.E 2 3.688 0.213

106 98 0.91 0.31 YES YES

SW:AACT_HUMAN alpha-1-antichymotrypsin 27 K.ITLLSALVETR.T 1 7.016 0.587 precursor (act) 94 98 1.19 0.49 YES YES

SW:APA4_HUMAN apolipoprotein a-iv precursor 26 K.SLAELGGHLDQQVEEFR.R 1 6.241 0.507 (apo-aiv) 69 49 0.95 0.34 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:IC1_HUMAN plasma protease c1 inhibitor 26 K.YPVAHFIDQTLK.A 1 4.724 0.481 precursor (c1 inh) (c1inh) 70 79 0.95 0.33 YES YES

SW:AFAM_HUMAN afamin precursor (alpha-albumin) 25 R.RHPDLSIPELLR.I 1 7.072 0.555 (alpha-alb) 131 100 1.02 0.4 YES YES

SW:CO6_HUMAN complement component c6 23 K.IEEADCK.N 1 5.490 0.437 precursor 37 34 1.36 0.18 YES YES

SW:APL1_HUMAN apolipoprotein l1 precursor 23 R.ANLQSVPHASASRPR.V 1 5.635 0.613 (apolipoprotein l-i) (apolipoprotein 68 52 1.18 0.38 YES YES

PIR1:I38344 titin, cardiac muscle [validated] - 23 K.RVDLIQDLPRVELQIK.E 1 2.584 0.145 human 22 15 0.5 0.31 YES

SW:APA2_HUMAN apolipoprotein a-ii precursor 23 K.AGTELVNFLSYFVELGTQPAT.Q 2 5.268 0.407 (apo-aii) (apoa-ii) 184 175 0.75 0.27 YES YES

SW:CLUS_HUMAN clusterin precursor (complement- 22 R.IDSLLENDR.Q 1 5.611 0.541 associated protein sp-40,40) 82 80 0.82 0.23 YES YES

GP:AF384856_1 Homo sapiens peptidoglycan 19 R.GSQTQSHPDLGTEGCWDQLSAPR.T 1 5.812 0.574 recognition protein L precursor 62 64 1.05 0.32 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:C1S_HUMAN complement c1s component 18 K.MGPTVSPICLPGTSSDYNLMDGDLG 1 4.507 0.527 precursor (ec 3 42 53 1.53 0.24 YES YES

SW:HBA_HUMAN hemoglobin alpha chain 17 K.KVADALTNAVAHVDDMPNALSALSD 1 6.655 0.524

89 63 0.63 0.1 YES YES

SW:HEP2_HUMAN heparin cofactor ii precursor (hc- 17 K.QFPILLDFK.T 1 2.074 0.237 ii) (protease inhibitor leuserpin 2) 58 53 1.03 0.33 YES YES

SW:CO7_HUMAN complement component c7 17 R.SYTSHTNEIHK.G 1 5.698 0.591 precursor 44 34 1.05 0.39 YES YES

SW:CO9_HUMAN complement component c9 17 R.DRDGNTLTYYR.R 1 5.048 0.56 precursor 35 41 1.09 0.34 YES YES

SW:APE_HUMAN apolipoprotein e precursor (apo-e) 15 R.AKLEEQAQQIR.L 1 5.699 0.471

75 66 1.09 0.32 YES YES

SW:CO8B_HUMAN Human complement component 15 R.SDLEVAHYK.L 1 6.445 0.581 C8-beta mRNA, partial cds. 37 44 1.2 0.39 YES YES

SW:ANGT_HUMAN angiotensinogen precursor 15 R.FMQAVTGWK.T 1 5.234 0.522 [contains: angiotensin i; 49 49 0.82 0.28 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:PON1_HUMAN serum paraoxonase/arylesterase 15 K.VTQVYAENGTVLQGSTVASVYK.G 1 6.381 0.481 1 (ec 3 79 56 1.32 0.45 YES YES

SW:C1R_HUMAN complement c1r component 14 R.WILTAAHTLYPK.E 1 5.213 0.578 precursor (ec 3 40 32 0.96 0.38 YES YES

GP:U82812_1 Human scavenger receptor 14 R.KPIWLSQMSCSGR.E 1 5.254 0.505 cysteine rich Sp alpha mRNA, 28 34 1.11 0.35

SW:CFAI_HUMAN complement factor i precursor (ec 14 K.SLECLHPGTK.F 1 5.814 0.591 3 38 34 0.93 0.27 YES YES

SW:A2AP_HUMAN alpha-2-antiplasmin precursor 14 K.QEDDLANINQWVK.E 2 5.987 0.543 (alpha-2-plasmin inhibitor) (alpha- 50 50 1.16 0.49 YES YES

SW:ACTG_HUMAN Actin, cytoplasmic 2 13 R.TTGIVMDSGDGVTHTVPIYEGYALPH 1 5.938 0.528

61 69 0.97 0.2 YES YES

SW:AMBP_HUMAN ambp protein precursor [contains: 12 K.KEDSCQLGYSAGPCMGMTSR.Y 1 5.553 0.598 alpha-1-microglobulin (protein hc) 29 26 1.01 0.27 YES YES

SW:CO2_HUMAN complement c2 precursor (ec 3 12 K.ALHQVFEHMLDVSK.L 1 5.646 0.495

32 30 0.82 0.28 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:CBP8_HUMAN carboxypeptidase n 83 kda chain 12 K.LGSLQELFLDSNNISELPPQVFSQLF 2 5.055 0.496 (carboxypeptidase n regulatory 28 19 0.68 0.22 YES YES

SW:PEDF_HUMAN pigment epithelium-derived factor 12 R.ALYYDLISSPDIHGTYK.E 1 5.074 0.499 precursor (pedf) (epc-1) 35 32 1.13 0.4 YES YES

SW:HBD_HUMAN hemoglobin delta chain 11 K.KVLGAFSDGLAHLDNLK.G 1 5.324 0.467

76 46 0.53 0.13 YES

SW:ZA2G_HUMAN zinc-alpha-2-glycoprotein 11 K.YYYDGKDYIEFNK.E 1 5.935 0.505 precursor (zn-alpha-2- 39 33 1.03 0.42 YES YES

SW:ATRN_HUMAN attractin precursor (mahogany 10 R.PDLHHDVNR.F 2 4.195 0.345 homolog) (dppt-l) 21 21 1.81 0.27 YES

SW:APC3_HUMAN apolipoprotein c-iii precursor 10 R.GWVTDGFSSLK.D 1 5.148 0.5 (apo-ciii) 57 51 0.62 0.15 YES YES

SW:SAA_HUMAN serum amyloid a protein 10 R.SGKDPNHFRPAGLPEK.Y 1 6.401 0.503 precursor (saa) [contains: amyloid 16 36 5.87 2.84 YES YES

SW:ALS_HUMAN insulin-like growth factor binding 10 R.LSHNAIASLRPR.T 1 4.915 0.544 protein complex acid labile chain 23 26 1.38 0.49 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:FA12_HUMAN coagulation factor xii precursor 10 R.NWGLGGHAFCR.N 1 5.357 0.524 (ec 3 19 18 1.11 0.42 YES YES

SW:PRTS_HUMAN vitamin k-dependent protein s 10 R.SCVNAIPDQCSPLPCNEDGYMSCK.D 1 5.267 0.557 precursor 45 38 1.11 0.4 YES YES

SW:FBL1_HUMAN fibulin-1 precursor 9 R.MVQEQCCHSQLEELHCATGISLANE 1 6.259 0.492

22 21 1.02 0.29 YES YES

SW:SAMP_HUMAN serum amyloid p-component 9 R.DNELLVYK.E 1 2.837 0.383 precursor (sap) (9 20 19 2.05 0.85 YES YES

GP:AF178534_1 Homo sapiens talin (TLN) gene, 9 K.AVSSAIAQLLGEVAQGNENYAGIAAR.D 2 6.106 0.491 exons 49 through 57 and 20 16 1.18 0.16

SW:A2GL_HUMAN leucine-rich alpha-2-glycoprotein 9 R.DGFDISGNPWICDQNLSDLYR.W 1 5.185 0.491 (lrg) 50 75 2.87 0.95 YES YES

SW:VWF_HUMAN von willebrand factor precursor 9 K.IPGTCCDTCEEPECNDITAR.L 2 3.945 0.32 (vwf) 3 13 1.06 YES YES

SW:FA5_HUMAN coagulation factor v precursor 9 R.QDGGKSRLKKSQFLIKTR.K 1 3.282 0.273 (activated protein c cofactor) 14 2 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:KAL_HUMAN plasma kallikrein precursor (ec 3 9 K.EIIIHQNYK.V 1 3.081 0.378

17 20 1.19 0.33 YES YES

SW:RETB_HUMAN plasma retinol-binding protein 9 K.YWGVASFLQK.G 1 2.915 0.252 precursor (prbp) (rbp) 28 22 0.99 0.34 YES YES

SW:ACTS_HUMAN actin, alpha 9 K.IWHHTFYNELR.V 1 4.613 0.4

34 23 1.19 0.44 YES YES

PIR2:I38346 Homo sapiens partial TTN gene 8 K.KPVPEEKVAVPVPVAKKAPPPR.A 1 2.105 0.145 for titin; Titin Isoform from 6 6 YES

PIR1:JC4795 plasma hyaluronan-binding 8 K.YSHYNERDEIPHNDIALLK.L 1 5.240 0.5 protein precursor - human 12 16 0.65 0.26 YES YES

SW:CO8A_HUMAN complement component c8 alpha 7 K.YNPVVIDFEMQPIHEVLR.H 1 4.664 0.475 chain precursor 21 21 0.87 0.18 YES YES

SW:THBG_HUMAN thyroxine-binding globulin 7 K.GTEAAAVPEVELSDQPENTFLHPIIQI 1 5.858 0.524 precursor (t4-binding globulin) 16 16 0.97 0.26 YES YES

SW:APOA_HUMAN apolipoprotein(a) precursor (ec 3 7 R.TPEYYPNAGLIMNYCR.N 1 5.01 0.535

12 14 0.83 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GPN:AF435011_1 Homo sapiens NUANCE (NUA) 7 K.KFILLLEFHYYK.C 1 2.809 0.075 mRNA, complete cds; actin- 8 4 YES

SW:KAIN_HUMAN kallistatin precursor (kallikrein 7 K.FSISGSYVLDQILPR.L 1 5.845 0.515 inhibitor) (protease inhibitor 4) 24 15 1.06 0.12 YES YES

SW:APOM_HUMAN apolipoprotein m (apom) (g3a) 7 K.SLTSCLDSK.A 1 4.952 0.478 (hspc336) 21 10 0.58 0.16

GP:V00494_1 Human messenger RNA for serum 6 K.KVPEVSTPTLVEVSR.N 1 3.994 0.473 albumin (HSA); reading frame 88 64 0.75 0.08

SW:ECM1_HUMAN extracellular matrix protein 1 6 K.TRPHWCCTR.Q 1 3.901 0.33 precursor (secretory component 7 6 0.64 YES YES

SW:LBP_HUMAN lipopolysaccharide-binding 6 R.VQLYDLGLQIHK.D 1 5.287 0.45 protein precursor (lbp) 7 27 2.55 1.44 YES YES

SW:ITH3_HUMAN inter-alpha-trypsin inhibitor heavy 6 K.GHVSFKPSLDQQR.S 1 3.635 0.398 chain h3 precursor 10 16 1.13 0.36 YES YES

SW:LUM_HUMAN lumican precursor (lum) (keratan 6 K.NIPTVNENLENYYLEVNQLEK.F 1 5.144 0.499 sulfate proteoglycan). 20 18 0.96 0.36 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:APOD_HUMAN apolipoprotein d precursor (apod) 6 K.CPNPPVQENFDVNK.Y 2 4.258 0.433

4 8 1.13 0.31 YES YES

SW:MYH9_HUMAN Homo sapiens mRNA for non- 6 R.KLEGDSTDLSDQIAELQAQIAELK.M 2 5.827 0.424 muscle myosin heavy chain. 13 4 0.57 0.04 YES YES

SW:MACF_HUMAN actin cross-linking family protein 7 6 R.GLNKPSKIPTMSKK.T 2 2.701 0.287 (macrophin) (trabeculin-alpha) 0 7

SW:APC2_HUMAN apolipoprotein c-ii precursor 6 K.ESLSSYWESAK.T 1 2.511 0.313 (apo-cii) 28 29 0.83 0.07 YES YES

SW:APC1_HUMAN apolipoprotein c-i precursor (apo- 6 K.LKEFGNTLEDK.A 1 3.421 0.307 ci) 37 31 1.33 0.08 YES

SW:ABP2_HUMAN endothelial actin-binding protein 6 K.VPVHDVTDASK.V 1 3.660 0.51 (abp-280) (nonmuscle filamin) 6 13 1.1 0.08

SW:A1AG_HUMAN alpha-1-acid glycoprotein 1 6 K.TYMLAFDVNDEK.N 1 4.318 0.506 precursor (agp 1) (orosomucoid 1) 47 35 1.09 0.33 YES YES

SW:TETN_HUMAN tetranectin precursor (tn) 6 K.DVVNTK.M 1 4.993 0.52 (plasminogen-kringle 4 binding 13 12 1.15 0.08 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:F13A_HUMAN coagulation factor xiii a chain 5 R.LALETALMYGAK.K 1 4.482 0.411 precursor (ec 2 12 6 1.03 YES YES

SW:FA8_HUMAN coagulation factor viii precursor 5 K.NATALRLNHMSNKTTSSKN.M 2 2.260 0.08 (procoagulant component) 6 11 1.04 YES

SW:AHNK_HUMAN neuroblast differentiation 5 K.MPKLNIKAPKVSMPDVDLNLK.G 2 2.641 0.086 associated protein ahnak 3 5 YES

GP:AF283408_1 Homo sapiens candidate tumor 5 E.EFSCADGR.C 2 2.273 0.119 suppressor protein (LRP1B) gene, 2 3

SW:LMA1_HUMAN laminin alpha-1 chain precursor 5 C.QDCAPGYHR.G 1 2.025 0.104 (laminin a chain) 4 2

SW:CO8G_HUMAN complement component c8 5 R.AEATTLHVAPQGTAMAVSTFR.K 1 5.391 0.488 gamma chain precursor 17 24 2.21 0.27 YES YES

SW:TALI_HUMAN talin 5 K.LLAALLEDEGGSGRPLLQAAK.G 1 5.098 0.503

10 12 0.96 0.23

SW:HGFA_HUMAN hepatocyte growth factor activator 5 R.LHKPGVYTR.V 1 3.671 0.338 precursor (ec 3 2 8 3.82 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:C4BB_HUMAN c4b-binding protein beta chain 5 K.LIQEAPKPECEK.A 1 4.868 0.399 precursor 11 7 2.1 0.15 YES YES

SW:CBPN_HUMAN carboxypeptidase n catalytic 5 K.GMVLDENYNNLANAVISVSGINHDVT 2 5.948 0.518 chain precursor (ec 3.4.17.3) 20 20 0.77 0.13 YES YES

GP:AJ417564_1 Homo sapiens mRNA for 5 K.FIIEGMEEAGSVALEELVEK.E 1 3.985 0.422 glutamate carboxypeptidase-like 9 4 1.91 YES

SW:HBB_HUMAN hemoglobin beta chain 5 R.FFESFGDLSTPDAVMGNPK.V 1 4.650 0.486

31 22 0.84 0.32 YES YES

GP:AB067480_1 Homo sapiens mRNA for 5 K.ADPVPLESMDSAS.T 1 1.851 0.113 KIAA1893 protein, partial cds; 5 3

SW:MYH3_HUMAN myosin heavy chain, fast skeletal 5 A.NSLAAALDKK.Q 1 2.026 0.077 muscle, embryonic (muscle 1 4

PIR2:T00062 hypothetical protein KIAA0434 - 5 A.LPPNSLVRK.V 1 2.047 0.125 human (fragment) 6 2

SW:NEBU_HUMAN Nebulin 4 K.NYKAEYEEDRGKGFFPQTITQ.E 2 2.889 0.14

4 10 1.27 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF055136_1 Homo sapiens alpha-tectorin 4 R.GKPVVSSVVLAQSWKTNGMQK.R 2 2.205 0.088 (TECTA) gene, exon 23 and 4 2 3.46

PIR2:T02435 Homo sapiens OSBP-related 4 G.SRPGSESSSGVGAGPFTK.A 1 2.171 0.062 protein 4 mRNA, complete cds; 2 4

GP:BC007057_1 Homo sapiens, carboxypeptidase 4 K.IHIGSSFEK.Y 1 4.607 0.462 B2 (plasma), clone MGC:12495 15 10 0.9 0.3 YES

SW:PRTZ_HUMAN vitamin k-dependent protein z 4 R.YDADAGENDLSLLELEWPIQCPGAG 1 2.739 0.264 precursor 3 2

SW:IF38_HUMAN eukaryotic translation initiation 4 K.GTTEEVCRIYLLRILHTY.Y 2 2.428 0.051 factor 3 subunit 8 (eif3 p110) 2 2

SW:BIR6_HUMAN baculoviral iap repeat-containing 4 I.EPSSEGSK.P 2 2.445 0.157 protein 6 (ubiquitin-conjugating 5 3

SW:SAA4_HUMAN serum amyloid a-4 protein 4 K.EALQGVGDMGR.A 1 5.645 0.501 precursor (constitutively 36 22 0.82 0.3 YES YES

PIR2:T02632 Homo sapiens PCAF-associated 4 K.NYSIAQK.R 1 1.980 0.138 factor 400 (PAF400) mRNA, 4 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:KI67_HUMAN cell proliferation antigen Ki-67, 4 K.PAVGEEKDINTFLGTPVQK.L 2 2.237 0.124 short form - human 1 3

GP:AF311312_1 Homo sapiens infertility-related 4 E.DLSKVLDVEPDNDLAK.K 1 2.184 0.064 sperm protein mRNA, complete 3 4 1.22

GP:Z93783_2 Human DNA sequence from clone 4 I.VDTDHQLLR.D 2 2.462 0.183 RP5-1042K10 on chromosome 3 3

SW:F13B_HUMAN coagulation factor xiii b chain 4 K.VLHGDLIDFVCK.Q 1 4.472 0.492 precursor (ec 2 9 11 1.34 0.5 YES

SW:CHLE_HUMAN cholinesterase precursor (ec 3 4 R.AILQSGSFNAPWAVTSLYEAR.N 2 4.411 0.516

0 10 YES

GP:U42594_1 Human fibronectin (FN1) mRNA, 4 V.YAQNPSGESQPLVQTAVTTIPAPTDL 2 4.613 0.491 splice variant, partial cds; Variant 10 2

SW:ZPI_HUMAN protein z-dependent protease 4 K.WLTPFDPVFTEVDTFHLDK.Y 2 4.518 0.392 inhibitor precursor 4 8 0.62 YES

SW:PROP_HUMAN properdin precursor 4 K.GLLGGGVSVEDCCLNTAFAYQK.R 2 4.435 0.449

4 4 0.71 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:SMCX_HUMAN smcx protein (xe169 protein) 4 H.FTPRIQR.L 2 2.392 0.142

4 3

SW:FA9_HUMAN coagulation factor ix precursor 4 R.VVGGEDAKPGQFPWQVVLNGK.V 2 5.571 0.504 (ec 3 6 7 3.11 YES YES

SW:CFAD_HUMAN complement factor d precursor 4 K.VQVLLGAHSLSQPEPSKR.L 2 4.837 0.456 (ec 3 10 6 1.31 YES

GP:AF075587_1 Homo sapiens protein associated 4 G.VIQLEK.E 1 2.185 0.076 with Myc mRNA, complete cds; 4 1

PIR2:T00051 hypothetical protein KIAA0404 - 4 I.MDTSTFLLR.F 1 2.396 0.067 human (fragment) 1 3

SW:FETA_HUMAN alpha-fetoprotein precursor 4 D.FAEEGQK.H 1 2.781 0.187 (alpha-fetoglobulin) (alpha-1- 7 9 1.16

GP:BC010634_1 Homo sapiens, step II splicing 4 S.RHGTVIKGQERAVACSK.Y 2 2.513 0.134 factor SLU7, clone MGC:9280 3 5

SW:BGH3_HUMAN transforming growth factor-beta 4 R.LTLLAPLNSVFK.D 1 4.917 0.454 induced protein ig-h3 precursor 5 7 0.75 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:G01627 Human DNA sequence from clone 4 R.PPSNGGAKETSHASLPQPEPPGGG 1 2.313 0.086 RP4-597B2 on chromosome 22 3 3

GP:AJ292757_1 Homo sapiens TUBB1 gene for 4 R.VSEHFSAMFK.R 1 5.155 0.398 human beta tubulin 1, class VI; 6 3 2.29

GP:X01794_1 Human haptoglobin related (Hpr) 4 K.VVLHPNYHQVDIGIIK.L 1 4.570 0.462 gene exon 1, and joined CDS. 16 18 0.96 YES

SW:APF_HUMAN apolipoprotein f precursor (apo-f) 4 R.SGVQQLIQYYQDQK.D 1 5.104 0.416

6 11 0.57 0.29 YES YES

SW:IMB3_HUMAN importin beta-3 subunit 4 A.EGEMHEAIKHEDPCAK.R 1 2.641 0.11 (karyopherin beta-3 subunit) (ran- 4 0

SW:LMA3_HUMAN laminin alpha-3 chain precursor 4 K.IGKLQKRMWINVDVQNTIIDGEVFDF.S 3 4.177 0.086 (epiligrin 170 kda subunit) (e170) 3 4

SW:CBG_HUMAN corticosteroid-binding globulin 4 R.ITQDAQLK.S 1 4.420 0.504 precursor (cbg) (transcortin) 20 26 1.09 0.38 YES YES

SW:CA1E_HUMAN collagen alpha 1(xv) chain 4 K.KLQLGELIPIPADSPPPPALSSN.P 2 2.206 0.082 precursor 1 5 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:T17272 hypothetical protein 4 K.EKEHKNQDDLLK.E 1 1.942 0.081 DKFZp434B0435.1 - human 4 3

SW:PLEK_HUMAN pleckstrin (platelet p47 protein) 4 R.KSEEENLFEIITADEVHYFLQAATPK. 1 5.597 0.348

14 7 0.31

PIR2:T00385 KIAA0624 protein - human 4 D.RENQEEFLRAPSPMEIDPADK.Y 2 2.200 0.073 (fragment) 3 5 0.71

GP:AL158167_3 Homo sapiens archvillin (SVIL) 3 K.FMVSTAVGS.R 1 2.047 0.135 mRNA, complete cds; muscle- 3 1

GP:BC001657_1 Homo sapiens, clone 3 K.KREQKKELGHVNGLVDK.S 1 2.531 0.151 IMAGE:3356959, mRNA, partial 3 2

GP:AB020671_1 Homo sapiens mRNA for 3 R.EGHQQGTAKLDQGAPGVKRQR.I 2 1.946 0.12 KIAA0864 protein, partial cds. 1 2

SW:MM20_HUMAN matrix metalloproteinase-20 3 F.APGEGLGGDTHFDNPEK.W 1 2.357 0.123 precursor (ec 3 0 5

SW:CRCM_HUMAN colorectal mutant cancer protein 3 K.YESNATALRLALQ.Y 1 2.631 0.068 (mcc protein) 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB033082_1 Homo sapiens mRNA for 3 E.KTQEKIQEEERK.A 1 1.844 0.052 KIAA1256 protein, partial cds; 3 1

GP:AL136611_1 Homo sapiens mRNA; cDNA 3 F.VPRSLKIKRNANDDGK.S 1 2.472 0.062 DKFZp564B1023 (from clone 1 3

GP:AB002306_1 Human mRNA for KIAA0308 gene, 3 K.ADASSGSDSTSSSSEDSDSSNED.- 2 2.047 0.062 partial cds. 2 2

GP:AF148216_1 Mus musculus serine protease 3 R.WILTAAHTIYPK.H 1 2.360 0.289 mRNA, complete cds; similar to 2 4 1.15

SW:MAPB_HUMAN microtubule-associated protein 1b 3 E.SVKKDSVAAGKPKEKGK.I 2 3.035 0.128 (map 1b) [contains: map1 light 1 3 YES

SW:G3P2_HUMAN glyceraldehyde 3-phosphate 3 K.AGAHLQGGAK.R 1 3.812 0.453 dehydrogenase, liver (ec 1 4 8 0.99

GP:Y16961_1 Homo sapiens mRNA for KET 3 P.PPYPTDCSIVSFLAR.L 2 2.229 0.128 protein. 2 1

GP:BC007978_1 Homo sapiens, clone MGC:14999 3 K.GIMQLVGQAEPESVLLVHGEAKKME.F 3 4.254 0.118 IMAGE:3836956, mRNA, complete 3 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB020522_1 Homo sapiens DLEC1 (deleted in 3 R.TRFSLKF.E 1 2.336 0.153 lung and esophageal cancer 1; 2 3

GP:AB011137_1 Homo sapiens mRNA for 3 Q.KEKKYFEDIEAVK.E 2 2.314 0.08 KIAA0565 protein, partial cds; 1 3

SW:FA10_HUMAN coagulation factor x precursor (ec 3 K.DGDQCETSPCQNQGK.C 2 3.530 0.378 3 5 6 1.53 YES

GP:BC006283_1 Homo sapiens, clone MGC:10685 3 A.NFCTGIELLVTGGAELGYGCK.A 2 3.389 0.274 IMAGE:4026397, mRNA, complete 9 4 1.75

GP:BC006474_1 Homo sapiens, clone 3 A.AEEIVDCITESLSILK.T 1 1.885 0.057 IMAGE:2820942, mRNA, partial 2 2

GPN:AF326352_1 Caenorhabditis elegans putative 3 K.AHSLTFTSSSRSSI.S 1 1.873 0.174 Rho guanine nucleotide exchange 3 5 3.38

SW:MLES_HUMAN P24572 homo sapiens (human), 3 K.VLDFEHFLPMLQTVAK.N 1 4.810 0.455 bos taurus (bovine), and sus 7 6 0.44

GP:U51583_1 Rattus norvegicus zinc finger 3 K.LHIVEEESVTDAADCEGGVPD.D 2 2.424 0.069 homeodomain enhancer-binding 3 5 0.72 0.7 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:SFR4_HUMAN splicing factor, arginine/serine- 3 K.RGSKRDSKAGSSKKKKKE.D 2 2.471 0.13 rich 4 (pre-mrna splicing factor 4 2

SW:ENC1_HUMAN ectoderm-neural cortex-1 protein 3 S.KEIVEEAIRCKLK.I 1 2.293 0.051 (enc-1) (p53-induced protein 10) 1 2

SW:DPOE_HUMAN dna polymerase epsilon, catalytic 3 A.IQKIITIPAALQQVKNPVPR.V 2 2.624 0.067 subunit a (ec 2 2 3

SW:SELP_HUMAN selenoprotein p precursor (sep) 3 R.HLIFEK.T 1 1.943 0.103

6 5 0.82 0.68 YES YES

SW:CHD4_HUMAN chromodomain helicase-dna- 3 K.NLKEGGHRVLIFSQMTK.M 1 1.869 0.115 binding protein 4 (chd-4) (mi-2 1 2

SW:CENE_HUMAN centromeric protein e (cenp-e 3 K.LQAKVHESNKCLEKTK.E 2 2.358 0.089 protein) 2 1

SW:AF17_HUMAN af-17 protein 3 K.MKTSRHSSGGGGGGAGGGGGSMG 2 2.037 0.064

2 3

PIR2:T09219 basal transcription factor SNAPc 3 A.FEELLVTK.W 1 1.922 0.108 large chain SNAP190 - human 4 1 0.54 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:S25409 transcription factor znf6 - human 3 A.SGNTLDSALESR.S 1 2.213 0.103

0 5

GP:AF302773_1 Homo sapiens ninein-Lm isoform 3 R.VLQDQVDELQ.S 1 2.925 0.1 (ninein) mRNA, complete cds; G- 4 1

SW:FCN3_HUMAN ficolin 3 precursor 3 R.ALPVFCDMDTEGGGWLVFQR.R 1 4.783 0.484 (collagen/fibrinogen domain- 12 9 1.48 0.71 YES YES

SW:XPD_HUMAN tfiih basal transcription factor 3 G.WCPYFLAR.Y 1 1.857 0.078 complex helicase subunit (ec 3 0

GP:AK001695_1 Homo sapiens mRNA for MOP-3, 3 T.IVMTKTPPVTTNRQTITLTK.F 2 3.013 0.266 complete cds; similar to a D. 6 3 0.15

GP:AF093637_1 Drosophila melanogaster SET 3 K.LLWGPVGYRCMDCGNSYHEKCTEH 3 3.794 0.121 domain binding factor (sbf) mRNA, 3 0

SW:LRP2_HUMAN low-density lipoprotein receptor- 3 R.TGSLLPALPKLPSLSSLVK.P 2 1.903 0.094 related protein 2 precursor 0 4

SW:ITA3_HUMAN integrin alpha-3 precursor 3 R.QPQQVIHGEK.L 1 1.849 0.091 (galactoprotein b3) (gapb3) (vla-3 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF205075_1 Homo sapiens organic anion 3 G.FLLCAIAMFLVIFPMFTFPKK.L 3 3.808 0.071 transporter polypeptide-related 0 3

SW:GPV_HUMAN platelet glycoprotein v precursor 3 R.LVSLDSGLLNSLGALTELQFHR.N 2 2.710 0.139 (gpv) (cd42d) 7 4 1.15

GP:AF317653_1 Homo sapiens G protein-coupled 3 T.AVWAAAGLLGALSLLGPPPAPPPAP 2 2.516 0.083 receptor (GPR62) gene, complete 3 1

SW:ABC2_HUMAN atp-binding cassette, sub-family 3 L.VSDTSTELSYILPSEAAKKGAFER.L 2 2.733 0.161 a, member 2 (atp-binding cassette 5 2

SW:CIQ1_HUMAN voltage-gated potassium channel 3 K.CPFSLELAEGGPAGGALYAPIAPGAP 2 2.486 0.145 protein kqt-like 1 (kvlqt1) (kv1 4 2 7.75

SW:AT7B_HUMAN copper-transporting atpase 2 (ec 3 3 K.PGSTVIARSINAH.G 1 2.232 0.112

4 1 YES

PIR2:JC4636 transcription elongation factor B 3 P.AGADLAK.L 1 2.209 0.097 chain 3, elongin A - human 1 6

GP:AF123658_1 Homo sapiens clone G3612 FEZ1 3 K.GLELEVCENELQRK.K 2 2.225 0.06 (FEZ1) mRNA, alternatively 1 4 5.11 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AL034420_1 Human DNA sequence from clone 3 A.PSSSSKVPTPLPSIHSASPTLGFAMM 2 2.762 0.096 RP5-1112F19 on chromosome 3 4

SW:PK3B_HUMAN phosphatidylinositol 3-kinase c2 3 C.NTFNADFQTAVPGSR.K 1 2.198 0.054 domain-containing beta 2 1

GP:AL031118_1 Human DNA sequence from clone 3 L.TVHQRIHQR.E 2 2.470 0.131 RP1-153G14 on chromosome 5 3 0.46

GP:AJ251506_1 Homo sapiens mRNA for organic 3 K.FKLSLVGIAKFSFLTSMISFL.F 2 2.426 0.085 anion transporter 8 (SLC21A8 1 4 YES

GP:AJ006778_1 Homo sapiens mRNA for DRIM 3 K.KHLPEPVAIK.F 2 2.404 0.112 protein. 3 1

SW:RN5A_HUMAN 2-5a-dependent ribonuclease 3 A.HLADFDKSIKWAGDPQEVK.R 2 3.451 0.068

3 1

GP:AF321191_1 Homo sapiens L-periaxin (PRX) 3 R.GLKAEAVK.G 1 1.802 0.084 mRNA, complete cds, alternatively 1 5

SW:TAG2_HUMAN transgelin 2 (sm22-alpha 3 R.YGINTTDIFQTVDLWEGK.N 2 4.100 0.454 homolog) 7 3 0.7 0.25 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF285605_1 Homo sapiens testis protein 3 K.SMASSVSKSHPTTSH.M 1 1.952 0.071 TEX15 (TEX15) mRNA, complete 2 2

SW:UBA1_HUMAN ubiquitin-activating enzyme e1 3 R.GGIVSQVKVPKKISFK.S 1 2.498 0.081 (a1s9 protein) 3 2 3.95

SW:DYR3_HUMAN dual-specificity tyrosine- 3 L.GSKLPPVVGIANK.L 1 1.828 0.083 phosphorylation regulated kinase 1 3

GP:AF356519_1 Homo sapiens axonemal dynein 3 A.SAVLETITNIQPK.E 1 2.097 0.116 heavy chain 8 (DNAH8) mRNA, 2 2

SW:DYHC_HUMAN dynein heavy chain, cytosolic 3 D.SVLSNVEVTLNVLADSVLMEQPPLR 2 2.857 0.062 (dyhc) (cytoplasmic dynein heavy 2 2

GP:AF121141_1 Homo sapiens endocrine regulator 3 K.QKESLRGSIPAAQVPVQVSIPSLIRY 2 2.449 0.106 mRNA, complete cds. 3 3

PIR2:A47161 Mac-2-binding glycoprotein 3 R.ASHEEVEGLVEK.I 1 5.489 0.539 precursor - human 11 9 1.06 0.19 YES

GP:AF043725_1 Homo sapiens PHD-finger protein 3 K.ALRPPSSPGVFGALQSFKE.D 2 2.668 0.142 (GRC5) mRNA, complete cds. 4 3 1.38 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF036382_1 Fugu rubripes MLL (MLL) gene, 3 R.LRATKLSPLKSRLKTLPGVPRRR.R 2 2.524 0.061 complete cds; similar to human 2 2

GP:AB046846_1 Homo sapiens mRNA for 3 K.HRVSFQPKLSPDLTRLK.E 2 2.844 0.08 KIAA1626 protein, partial cds; 1 2

SW:CA12_HUMAN collagen alpha 1(ii) chain 3 P.GPAGEEGKRGARGEPGGVGPIGPP 2 2.268 0.176 precursor [contains: chondrocalcin] 2 2

GP:AB037837_1 Homo sapiens mRNA for 3 K.GSEEDEEEKLEDDD.K 2 2.728 0.072 KIAA1416 protein, partial cds; 1 3

SW:CA25_HUMAN collagen alpha 2(v) chain 3 R.GENGPTGAVGFAGPQGPDGQ.P 2 2.362 0.165 precursor 6 2 0.96

SW:Z267_HUMAN zinc finger protein 267 (zinc finger 3 K.PYKCKECGKAFRCSSYLTKHKR.I 2 2.822 0.082 protein hzf2) (fragment) 0 3

SW:PDX3_HUMAN mitochondrial thioredoxin- 3 K.DLSLDDFK.G 1 2.264 0.14 dependent peroxide reductase 2 4 1.28 0.5 YES YES

GP:AF231022_1 Homo sapiens protocadherin Fat 2 3 R.FLSHKLDIK.R 2 2.171 0.069 (FAT2) mRNA, complete cds; 12 5 0.55 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:GSHP_HUMAN plasma glutathione peroxidase 3 K.NSCPPTSELLGTSDR.L 2 3.591 0.424 precursor (ec 1 2 4 YES

SW:Y553_HUMAN hypothetical protein kiaa0553 3 R.ERSRSRGRSRSSSCSRSRSKR.R 2 2.379 0.235

2 2

GP:AJ012737_1 Homo sapiens mRNA for filamin, 3 R.GQHVPGSPFQFTVGPLGEGGAHK.V 2 4.016 0.385 muscle isoform. 8 2 0.71

SW:K1CM_HUMAN keratin, type i cytoskeletal 13 3 A.RVSAGGSSFSSGSRCGLGGSSAQG 2 2.763 0.096 (cytokeratin 13) (k13) (ck 13) 3 0

GP:M73548_1 Human polyposis locus (DP2.5 3 L.KPGEKSTLETK.K 2 2.466 0.169 gene) mRNA, complete cds; 1 3

GP:AB059277_1 Homo sapiens mRNA for 3 F.MDPQTIQSIQQCYLLLSNLNIVLSCFA 3 3.860 0.243 transcription factor ELYS, 0 4

GP:AK023181_1 Homo sapiens cDNA FLJ13119 fis, 3 K.RKGLYVEE.K 1 2.676 0.145 clone NT2RP3002671, weakly 2 6 1.52

GP:D49835_1 Homo sapiens mRNA for DNA- 3 R.PGSGRPRPEKLAEETEGPSDGESA 3 3.256 0.188 binding protein, complete cds. 1 3 2.14 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:KF4A_HUMAN chromosome-associated kinesin 3 K.ELVELNKALALKEALARKMTQ.N 2 2.253 0.077 kif4a (chromokinesin) 3 1

GP:U70136_1 Human megakaryocyte stimulating 3 K.ETAPTTPKGTAPTTLK.E 1 2.267 0.195 factor mRNA, complete cds; MSF. 18 6 0.15 YES

PIR2:T42701 hypothetical protein 3 K.LHLQHQNVTCEK.E 2 2.336 0.158 DKFZp434G156.1 - human 3 1

PIR2:T46910 hypothetical protein 3 K.LGGKSPPPPPPPPRRSYLPGSGLT 3 3.838 0.119 DKFZp761L0424.1 - human 2 2

PIR2:T00346 hypothetical protein KIAA0583 - 3 M.LSSTAVPEKLSVYKKPK.Q 2 2.500 0.06 human (fragment) 3 2

PIR2:T00271 hypothetical protein KIAA0540 - 3 F.FIDQANYFLNFPCK.V 1 2.233 0.084 human (fragment) 0 3

GP:U80446_1 Caenorhabditis elegans cosmid 3 R.QLISSLKHEENELKK.T 2 2.079 0.188 F56A3, complete sequence; weak 0 8

GP:U49844_1 Human FRAP-related protein 3 A.LIRTLGKQLNVNR.R 2 2.267 0.124 (FRP1) mRNA, complete cds; 1 2 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:D86978_1 Human mRNA for KIAA0225 gene, 3 L.LYWDGKRCIANSLKALIQSR.R 3 3.902 0.177 partial cds; similar to a C.elegans 2 1

SW:ACE_HUMAN angiotensin-converting enzyme, 3 A.KRQQYNALLSNMSR.I 1 2.364 0.096 somatic isoform precursor (ec 3 2 1

SW:PF4L_HUMAN platelet basic protein precursor 3 K.GKEESLDSDLYAELR.C 1 5.359 0.528 (pbp) 11 4 1.5 YES

SW:PLF4_HUMAN platelet factor 4 precursor (pf-4) 3 K.ICLDLQAPLYK.K 1 3.423 0.413 (oncostatin a) (iroplact) 11 14 1.56 1.06 YES

SW:CATH_HUMAN cathepsin h precursor (ec 3 3 G.VPVCGAAELCVNSLEK.F 2 2.280 0.083

3 0

GP:AL513466_12 Neurospora crassa DNA linkage 3 D.PRERDFLKTTLHRIYGKFLNLRSFIR 3 3.779 0.115 group V BAC contig B18D24; 2 9 1.64

GP:AB037834_1 Homo sapiens mRNA for 3 K.RNENFPK.D 1 2.204 0.052 KIAA1413 protein, partial cds; 2 1

SW:TRAD_HUMAN umor necrosis factor receptor 3 E.ELAELEDALR.N 2 2.276 0.062 type 1 associated death domain 4 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF190168_1 Homo sapiens serum albumin 3 A.KQEPESNECFLQHKDDNPNLPR.L 2 2.490 0.182 precursor, mRNA, complete cds. 4 1

GP:J00127_1 Human fibrinogen alpha-chain 3 R.NPGSSGTGGTATWKPGSSGPGSA 3 6.883 0.522 mRNA, complete cds; alpha- 16 18 1.95 1.21

GP:M14162_1 Human apolipoprotein B-100 3 K.AVSMPSFSIIGSDVR.V 1 5.354 0.426 mRNA, complete cds; 5 5 1.21 0.28

GP:AY032950_1 Homo sapiens LTRPC7 (LTRPC7) 2 K.TFNFGQNEALHLFQT.L 2 2.625 0.284 mRNA, complete cds; member of 14 17 1.68

SW:CA24_HUMAN collagen alpha 2(iv) chain 2 K.GIDGMPGTPGLKGDRGSPGMDGFQ 2 2.577 0.057 precursor 1 3 2

SW:RBL2_HUMAN retinoblastoma-like protein 2 (130 2 K.QIKTFAMKYSQAN.M 2 2.320 0.121 kda retinoblastoma-associated 2 1

SW:CA44_HUMAN collagen alpha 4(iv) chain 2 K.GSSPVGPPGPPGSPGVNGQKGIPG 2 2.03 0.12 precursor 4 0

SW:CADD_HUMAN cadherin-13 precursor 2 K.PSPNMFYIDPEKGDIVTVVSPAL.L 2 3.019 0.1 (truncated-cadherin) (t-cadherin) 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:CRBS_HUMAN beta crystallin s (gamma crystallin 2 R.QYLLDKK.E 2 2.721 0.069 s) 2 0

SW:RBB1_HUMAN retinoblastoma-binding protein 1 2 E.EDMEPCLTGTKVK.V 1 2.551 0.13 (rbbp-1) 1 2 1.02

SW:DOPO_HUMAN dopamine beta-monooxygenase 2 R.LEVHYHNPLVIEGR.N 2 2.670 0.312 precursor (ec 1 2 3 YES

SW:MLH3_HUMAN dna mismatch repair protein mlh3 2 K.ESGQLPNKK.N 1 1.898 0.073 (mutl protein homolog 3) 0 5

SW:PRKD_HUMAN dna-dependent protein kinase 2 D.PIIAKQLFSSLFSGILKEMDK.F 2 2.431 0.051 catalytic subunit (ec 2 3 3 1.2

SW:PER1_HUMAN period circadian protein 1 2 F.RLTPYVTKIR.V 1 1.963 0.16 (circadian pacemaker protein 1 1

SW:PCFB_HUMAN pre-mrna cleavage complex ii 2 I.FPLKK.L 1 1.862 1 protein pcf11 (fragment) 1 1

SW:ECHM_HUMAN enoyl-coa hydratase, 2 D.RKEGMTAFVEK.R 1 2.357 0.082 mitochondrial precursor (ec 4 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:CABI_HUMAN calcineurin-binding protein cabin 1 2 L.MKFLPSRLR.K 2 2.211 0.055 (calcineurin inhibitor) (cain) 0 1 1.41

SW:ORC2_HUMAN origin recognition complex subunit 2 E.FRDHKLIR.T 1 2.756 0.107 2 6 4 0.55 0.16

SW:NP14_HUMAN nucleolar phosphoprotein p130 2 E.EKKPPTKAVVSK.A 2 3.175 0.151 (nucleolar 130 kda protein) (140 1 2

SW:LMA2_HUMAN laminin alpha-2 chain precursor 2 K.FSGAKCTECSR.G 1 2.048 0.14 (laminin m chain) (merosin heavy 1 2

SW:NOP5_HUMAN nucleolar protein nop5 (nucleolar 2 K.AKIKVKVEEE.E 1 2.261 0.073 protein 5) (nop58) (hspc120) 0 4

SW:LMA4_HUMAN laminin alpha-4 chain precursor 2 A.SKIQVSMMFDGQSAVEVHSR.T 2 2.312 0.133

0 4

SW:N155_HUMAN nuclear pore complex protein 2 K.DHIPITDSPVVVQQHMLPPK.K 2 2.333 0.182 nup155 (nucleoporin nup155) 0 3

SW:DVL2_HUMAN segment polarity protein 2 D.GCEGRGLSVHTDMASVTK.A 2 2.687 0.138 dishevelled homolog dvl-2 2 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:SC31_HUMAN neutral and basic amino acid 2 L.TKGVDGFSLDAVKFLLEAKHLR.D 2 2.450 0.055 transport protein rbat (b(0,+)-type 2 1

GP:AB007932_1 Homo sapiens mRNA for 2 L.IIVIIVLIAYKR.K 1 1.944 0.058 KIAA0463 protein, partial cds. 0 3

GP:AL035425_2 Human DNA sequence from clone 2 R.PPEREDSDNDDDTHVR.M 1 2.250 0.15 RP6-24A23 on chromosome 1 1

GP:BC000102_1 Homo sapiens, Similar to collagen, 2 K.KKSHFGGPDYEEGPNSLIN.E 2 2.216 0.151 type IV, alpha 3 (Goodpasture 0 2

GP:BC004143_1 Homo sapiens, B-factor, 2 P.WSLAWPQGSCSLEGVEIK.G 2 3.114 0.3 properdin, clone MGC:1795 3 2 0.9

GP:D38024_1 Human facioscapulohumeral 2 C.PPEGGLLLTSLRPPKGWPCR.L 2 2.561 0.143 muscular dystrophy (FSHD) gene 0 3

GP:D21239_1 Homo sapiens mRNA for C3G 2 K.PDGPAELPLTDR.E 1 1.895 0.091 protein, complete cds; 1897-2047 3 0

GP:AB003723_1 Homo sapiens mRNA for GPI1, 2 A.SGPICLLLASLLSLVSAVSACRVFK.L 2 2.798 0.157 complete cds. 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC008014_1 Homo sapiens, Similar to kinesin 2 K.KCHNELVRLKGNIRVIARVRPVTKED 3 4.095 0.094 family member C3, clone 2 0 YES

SW:S3B1_HUMAN splicing factor 3b subunit 1 2 A.AGELK.N 1 1.931 0.114 (spliceosome associated protein 2 4 1.64

SW:M2GD_HUMAN dimethylglycine dehydrogenase, 2 E.TVIIGGGCVGVSLAYHLAK.A 2 2.883 0.086 mitochondrial precursor (ec 1 0 2

SW:CA1B_HUMAN collagen alpha 1(xi) chain 2 E.DGPEGPKGRAGPTGDPGPSGQAG 2 2.299 0.084 precursor 2 0

SW:RPB1_HUMAN dna-directed rna polymerase ii 2 K.LLVDSNNPKIKDILAKSK.G 2 3.060 0.091 largest subunit (ec 2 0 5

SW:CA15_HUMAN collagen alpha 1(v) chain 2 K.TVLEIDTPKVEQVPIADI.M 1 2.240 0.071 precursor 2 0

PIR2:G01449 probable mucin G2 [similarity] - 2 L.PAEGSDGSPPATRDLLLSSK.V 2 3.511 0.168 human (fragment) 7 8 1.94 1

SW:ROM_HUMAN heterogeneous nuclear 2 A.MQKAGRLGSTVFVANLDYKVGWK.K 2 2.390 0.076 ribonucleoprotein m (hnrnp m) 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:AMPE_HUMAN glutamyl aminopeptidase (ec 3 2 R.RCFEYKK.Q 2 2.246 0.085

2 0 YES

SW:BTD_HUMAN biotinidase precursor (ec 3 2 K.SHLIIAQVAK.N 1 4.276 0.509

8 6 1.48 0.338

SW:RFX1_HUMAN mhc class ii regulatory factor rfx1 2 K.HCDNVLYQGLVEILIPDVLRPIP.S 2 2.723 0.082 (rfx) (enhancer factor c) (ef-c) 1 1

SW:SC63_HUMAN translocation protein sec63 2 K.KCPALLQEMVNVICQL.I 2 2.661 0.082 homolog 1 1

SW:A1A4_HUMAN sodium/potassium-transporting 2 N.QEILPIAK.R 1 1.882 0.071 atpase alpha-4 chain (ec 3 1 1

GP:Y00649_1 Human mRNA for B-lymphocyte 2 R.GSTPYRHGDSVTFACKTNFSMNGN 2 1.922 0.059 CR2-receptor (for complement 2 0

SW:CA14_HUMAN collagen alpha 1(iv) chain 2 K.GEKGQAGPPGIGIPGLR.G 2 2.163 0.085 precursor 2 2 YES

SW:MEC2_HUMAN methyl-cpg-binding protein 2 2 K.AFRSKVELIAYFEKVGDTSLDPNDFD 3 3.690 0.112 (mecp-2 protein) (mecp2) 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:RPOM_HUMAN dna-directed rna polymerase, 2 R.KLLTLDMYNAVMLGWAR.Q 2 2.866 0.086 mitochondrial precursor 0 4

GP:U40025_1 Streptococcus gordonii M5 cell 2 A.EDKYQEDLK.A 1 2.249 0.063 surface adhesin A (sspA) gene, 2 2

SW:LMG1_HUMAN laminin gamma-1 chain precursor 2 K.ELEVKNLLEK.G 1 2.355 0.068 (laminin b2 chain) 1 1

SW:B2MG_HUMAN beta-2-microglobulin precursor 2 K.VEHSDLSFSK.D 1 4.432 0.41

7 6 1.21 0.29 YES

GP:AB011422_1 Homo sapiens mRNA for Trad, 2 K.KCIHKATRK.D 1 1.844 0.09 complete cds. 2 1

SW:CPT7_HUMAN cytochrome p450 17 (ec 1 2 G.AKYPKSLLSLPLVGSLPFLPR.H 2 3.349 0.125

0 4

PIR2:I52882 autoantigen - human 2 K.MWCTVSWTCLQTIRFSPDIFSSVSV 2 2.195 0.073

3 1 0.59 YES

SW:COPA_HUMAN coatomer alpha subunit (alpha- 2 K.HAIVICNRKLDALCNIHENIRVKSGA. 2 2.208 0.106 coat protein) (alpha-cop) (hepcop) 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SWN:XPO4_HUMA exportin 4 (exp4) 2 K.YVREQILLAVAVIVK.R 2 3.284 0.166 N 2 1

GP:U90920_1 Human PTPL1-associated 2 L.ENLVIICGHQK.L 1 2.381 0.086 RhoGAP mRNA, complete cds; 6 9 2.58

SW:TNFB_HUMAN tymphotoxin-alpha precursor (lt- 2 P.GAQGLPGVGLTPSAAQTARQHPK.M 2 2.518 0.079 alpha) (tnf-beta) 0 3

GP:AF117754_1 Homo sapiens thyroid hormone 2 G.QESVTSVTELMVQCKK.P 2 2.633 0.136 receptor-associated protein 4 0 YES

GP:U77129_1 Human SPS1/STE20 homolog 2 -.MEAPLRPAADILRR.N 2 2.267 0.064 KHS1 mRNA, complete cds; 2 2

GP:BC004542_1 Homo sapiens, clone MGC:11315 2 K.LFKAIKHQ.V 1 2.199 0.167 IMAGE:3951420, mRNA, complete 4 4 2.45

GP:U19033_1 Mus musculus Smage-3 protein 2 R.ATEQEVWQFLHGVGVYAGKKHLIFG 2 2.554 0.057 gene, complete cds; similar to 2 2

SW:NEST_HUMAN nestin 2 G.EGHPENPEPK.E 1 2.393 0.122

2 5 0.98 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK023503_1 Homo sapiens cDNA FLJ13441 fis, 2 K.ILHAGFKMMSKERLLALK.R 2 2.295 0.078 clone PLACE1002775, weakly 0 3

GP:AK024084_1 Homo sapiens cDNA FLJ14022 fis, 2 K.LGNHPVHR.V 2 2.312 0.241 clone HEMBA1003538, weakly 2 2 YES

GP:AK024441_1 Homo sapiens mRNA for 2 R.NHDSSQPTTPSQSSAASTPAPNLP 2 3.242 0.084 FLJ00031 protein, partial cds; 2 0

GP:AK024460_1 Homo sapiens mRNA for 2 K.KVELKENLIAE.L 2 2.571 0.057 FLJ00052 protein, partial cds; 1 1

GP:AK025571_1 Homo sapiens cDNA: FLJ21918 2 K.DLLSVFQAYQLPADDYTSLMPVGDP 2 2.741 0.064 fis, clone HEP04006; unnamed 1 2

GP:AK025577_1 Homo sapiens cDNA: FLJ21924 2 R.KRLLLNLHLDQSFK.N 2 2.525 0.091 fis, clone HEP04086; unnamed 2 5 8.34

GP:AK026281_1 Homo sapiens cDNA: FLJ22628 2 N.WSNSTCLKLAVSGGLR.P 1 2.125 0.073 fis, clone HSI06177; unnamed 2 0

GP:AK026804_1 Homo sapiens cDNA: FLJ23151 2 L.KIKFNKIAAEFKK.E 1 2.481 0.114 fis, clone LNG09417; unnamed 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK026973_1 Homo sapiens cDNA: FLJ23320 2 I.CQDWSHCSLSEALLDLSDHRR.N 2 2.887 0.117 fis, clone HEP12381; unnamed 1 1

GP:L25068_1 Schistosoma mansoni amino acid 2 K.DSNATESVALKKEVSVLQGVS.I 2 2.207 0.056 permease (PRM1) mRNA, 1 1

SW:MPN_HUMAN marapsin precursor (ec 3 2 L.CAGFEEGKK.D 1 1.984 0.13

3 1 2

GP:U12978_1 Homo sapiens BS-84 (HSD-1) 2 L.AQAGTPAPTK.P 1 1.844 0.155 mRNA, complete cds. 0 3

SW:PAC4_HUMAN paired basic amino acid cleaving 2 D.AEALVVEAKKWTAVPSQHMCVAAS 2 2.432 0.075 enzyme 4 precursor (ec 3 2 0

SW:MCM4_HUMAN dna replication licensing factor 2 A.AAEDIVASEQSLGQK.L 1 2.646 0.149 mcm4 (cdc21 homolog) (p1- 2 1

GP:AJ272208_1 Homo sapiens mRNA for IL-1 2 I.KLLSLIK.W 1 1.902 1 receptor accessory protein-like 2 3 3 0.51 0.3

GP:AB013380_1 Homo sapiens mRNA for mono 2 R.GLKGQAVAFIRNFPQGFNTVVG.E 2 2.267 0.063 ATP-binding cassette protein, 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF009014_1 Homo sapiens glutamate receptor 2 H.IPHLFIQR.S 1 2.304 0.071 delta-2 subunit (GLURD2) mRNA, 1 3 2.01

SW:TRDN_HUMAN triadin 2 A.AKKDEKKEDSKKTKKPAEVEQPKG 3 3.976 0.193

3 0

GP:AF317652_1 Homo sapiens G protein-coupled 2 L.LDLTAVAGNAAVMAVIAKTPALR.K 2 2.224 0.076 receptor (GPR61) mRNA, 1 1

GP:AB053450_1 Homo sapiens mRNA for 2 R.VCVDTHVRSTCYGAIEK.G 2 2.795 0.129 KIAA1776 protein (fibrillin3), 1 1

GP:AF163302_1 Homo sapiens somatostatin 2 K.PESPLTPGPP.H 1 1.826 0.112 receptor interacting protein splice 1 1

SW:GNRP_HUMAN guanine nucleotide releasing 2 K.NGVISLIDCTLLEEPE.S 2 2.207 0.108 protein (gnrp) (ras-specific 0 2

SW:AAC1_HUMAN alpha-actinin 1 (alpha-actinin 2 R.KHEAFESDLAAHQDR.V 2 3.984 0.425 cytoskeletal isoform 3 2

PIR2:T00075 hypothetical protein KIAA0461 - 2 I.EDSVVEDYNSVDK.T 1 2.078 0.088 human (fragment) 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:VDR_HUMAN vitamin d3 receptor (vdr) (1,25- 2 R.VNDGGGSHPSR.P 2 1.904 0.072 dihydroxyvitamin d3 receptor) 0 4

SW:TRP4_HUMAN short transient receptor potential 2 H.DWWNLMDFVMNSLYLATISLK.I 2 2.671 0.154 channel 4 (trpc4) (trp-related 0 3

GP:S67071_1 U1 small nuclear ribonucleoprotein 2 D.EDSDDVPRKRK.L 1 2.379 0.156 1SNRP homolog [human, thyroid 1 2

SW:RYR2_HUMAN ryanodine receptor 2 (cardiac 2 K.EAATPEEESDTLEK.E 1 3.676 0.191 muscle-type ryanodine receptor) 11 3 0.52

GP:AF118108_1 Homo sapiens lymphatic 2 K.NEAAGFGGVPTALLVLALLFFGAAAG 2 3.008 0.166 endothelium-specific hyaluronan 2 0

SW:PTPB_HUMAN protein-tyrosine phosphatase 2 K.VDSQTIPKHV.F 1 2.060 0.071 beta precursor (ec 3 3

SW:PEC1_HUMAN platelet endothelial cell adhesion 2 E.KLELNEKMVKLK.R 2 3.669 0.093 molecule precursor (pecam-1) 4 3 0.76

GP:AK056557_1 Homo sapiens partial mRNA for 2 K.YTCIASNEAGEVSKHFILKVLEPPH.I 2 2.365 0.073 fibulin-6 (FIBL-6 gene). 0 2 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:TRIB_HUMAN thyroid receptor interacting protein 2 L.QRHPDCANVKQWK.G 1 1.936 0.091 12 (trip12) 0 3

GP:AK025639_1 Homo sapiens cDNA: FLJ21986 2 E.ITWQPHNCQYGVLTKPQLQQCLGG 2 2.461 0.161 fis, clone HEP06248; unnamed 2 0

SW:G6PI_HUMAN glucose-6-phosphate isomerase 2 K.GLHHKILVANF.L 1 2.265 0.116 (gpi) (ec 5.3.1.9) 1 2 3.06

GP:AF191340_1 Homo sapiens anaphase- 2 K.VRPSTGNSASTPQSQCLPSEIEV.K 2 2.392 0.139 promoting complex subunit 7 0 2

GP:AF221634_1 Homo sapiens dipeptidyl 2 R.ADSFRYPKTGTANPKVTFKM.S 2 2.706 0.069 peptidase 8 (DPP8) mRNA, 0 2

GP:AF262962_1 Homo sapiens VASA protein 2 R.PVLSGTGNGDTSQSRSGSGSERG 2 1.915 0.053 mRNA, complete cds. 2 0

SW:SYK_HUMAN lysyl-trna synthetase (ec 6.1.1.6) 2 R.KILDDICVAKAVECPPPRTTARLLDK.L 2 1.938 0.056 (lysine--trna ligase) (lysrs). 1 1

GP:AB018353_1 Homo sapiens mRNA for 2 R.ETDFMAFHQE.H 1 2.024 0.101 KIAA0810 protein, partial cds; 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB018283_1 Homo sapiens mRNA for 2 K.PLLICSCEWMAAMF.G 1 1.960 0.082 KIAA0740 protein, partial cds; 1 1

GP:AB018337_1 Homo sapiens mRNA for 2 R.KLSHLDYDITLQEAGLCPQETVFVQ 2 2.545 0.098 KIAA0794 protein, partial cds. 1 1

GP:AJ223075_1 Homo sapiens mRNA for TRIP 2 L.DEGVAKDNAK.I 1 2.018 0.111 protein. 1 2

GP:AK000283_1 Homo sapiens cDNA FLJ20276 fis, 2 K.SEMATMKVRSG.R 1 1.915 0.095 clone HEP02437; unnamed 3 0

GP:AB012851_1 Homo sapiens mRNA for Musashi, 2 E.QFGKVDDAMLMFDKTTNR.H 2 2.853 0.065 complete cds. 2 0

SW:ICE5_HUMAN caspase-5 precursor (ec 3 2 K.SFEVPQAK.A 1 2.218 0.095

3 1

GP:AK024002_1 Homo sapiens cDNA FLJ13940 fis, 2 H.QSSLQK.K 1 2.046 1 clone Y79AA1000833, 1 1

SW:RED_HUMAN red protein (rer protein) (ik factor) 2 R.RRKKKSYYAKLRQQEIERERELAEK 1 3.618 0.07 (cytokine ik) 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB020688_1 Homo sapiens mRNA for 2 R.AHLLETTPKAQHKSLLK.R 2 1.942 0.08 KIAA0881 protein, complete cds. 1 3 YES

GP:AK056303_1 Homo sapiens cDNA FLJ31741 fis, 2 R.ELFLTAGGAGGLHLWKYEYPIQR.S 2 2.213 0.082 clone NT2RI2007148; unnamed 1 1

GP:AL021391_1 Human DNA sequence from clone 2 K.LEEYTK.T 1 2.004 0.241 RP1-102D24 on chromosome 22 2 4 0.8

GP:AB023145_1 Homo sapiens mRNA for 2 R.TYDGKVRVTVEVVGKGKFKGVGR.S 2 3.049 0.152 KIAA0928 protein, partial cds. 3 2 0.77

SW:DCOR_HUMAN ornithine decarboxylase (ec 4 2 A.FYVADLGDILKKHLRWLKALPR.V 2 2.357 0.053

0 3

SW:DDH2_HUMAN ng,ng-dimethylarginine 2 K.LRQRLGLQLLELPP.E 1 2.238 0.072 dimethylaminohydrolase 2 (ec 3 4 0

SW:FLIH_HUMAN flightless-i protein homolog 2 G.RKSPRLVR.A 2 2.246 0.117

1 2

SW:FXR1_HUMAN fragile x mental retardation 2 F.VVREDLMGLAIGTHGSNIQQAR.K 2 3.131 0.073 syndrome related protein 1 0 3 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:GCST_HUMAN aminomethyltransferase, 2 I.SVPVAGAVHLATAILK.N 2 2.315 0.141 mitochondrial precursor 0 4

SW:HAN2_HUMAN heart- and neural crest 2 K.IKTLRLATSYIAYLM.D 2 2.953 0.122 derivatives-expressed protein 2 1 2

GP:AF005258_1 Homo sapiens laminin alpha 3b 2 P.CTRSCEARHFLLDGEPRPVAVR.Q 2 2.205 0.099 chain mRNA, partial cds; 1 1

SW:CP27_HUMAN Q02318 h cytochrome p450 27, 2 I.VLVPNK.K 1 2.152 0.063 mitochondrial precursor (ec 1 1 1

GP:AB040921_1 Homo sapiens mRNA for 2 K.ELAKDTRSDHLTVV.N 1 2.103 0.057 KIAA1488 protein, partial cds; 2 0 YES

SW:TGR3_HUMAN tgf-beta receptor type iii precursor 2 K.NFLSLNYLAEYLQPKAAEGC.V 2 2.688 0.056 (tgfr-3) (betaglycan) 0 2

GP:AF055084_1 Homo sapiens very large G- 2 D.PNGVVQFAPETLSK.K 2 2.646 0.065 protein coupled receptor-1 1 2 0.65

SW:CLDB_HUMAN claudin-11 (oligodendrocyte 2 G.CVILCCAGDAQAFGENVSTTLRALA 2 2.332 0.114 specific protein) 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF141870_1 Homo sapiens translational control 2 K.WFQARANGLKSCVIVIR.V 2 1.916 0.076 protein 80 mRNA, complete cds; 2 1

SW:B3G5_HUMAN beta-1,3-galactosyltransferas 2 H.RFCPQAAFVMK.T 1 2.415 0.086

2 3 1.09

GP:AF018167_1 Homo sapiens telomerase catalytic 2 K.NAGMSLGAKGAAGPLPSEAVQWLC 2 2.266 0.138 subunit (hEST2) mRNA, complete 1 1

SW:ZN43_HUMAN zinc finger protein 43 (zinc protein 2 E.ECGKAFNRCSHLTRHK.K 2 2.329 0.198 htf6) (zinc finger protein kox27) 1 1

SW:MIS_HUMAN muellerian inhibiting factor 2 R.LALDPDALAGFPQGLVNL.S 2 2.292 0.127 precursor (mis) (anti-muellerian 3 0

GP:AF110377_1 Homo sapiens PCAF-associated 2 Q.AAQQIIELQEAAQINAGLQPTNLGR.N 2 3.470 0.191 factor 400 (PAF400) mRNA, 4 1

GP:AB049586_1 Homo sapiens mRNA for beta-1,3- 2 K.LVFLLGVAGSAPPAQLL.A 1 2.385 0.273 N-acetylglucosaminyltransferase 2 2

SW:GDFF_HUMAN growth/differentiation factor 15 2 L.GSGGHLHLR.I 2 2.797 0.221 precursor (gdf-15) (placental bone 2 3 0.22 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF145710_1 Homo sapiens calcium/calmodulin- 2 I.EAISNGDFESYTK.M 2 2.276 0.08 dependent protein kinase II alpha 0 3

GP:AB040939_1 Homo sapiens mRNA for 2 R.ERPLLLEEQPLLLQDLLDQERQEQ 3 3.778 0.059 KIAA1506 protein, partial cds; 2 1

GP:AB011107_1 Homo sapiens mRNA for 2 C.PLPGCNGLGHVNNVFVTHR.S 2 2.352 0.092 KIAA0535 protein, complete cds. 1 1

SW:MK_HUMAN midkine precursor (neurite 2 N.AQCQETIRVTKPCTPKTK.A 2 2.933 0.125 outgrowth-promoting protein) (mk) 1 1

SW:PBEF_HUMAN pre-b cell enhancing factor 2 K.QNFIPHTSLQVKNSQ.L 2 2.660 0.115 precursor 2 1

SW:BMR2_HUMAN bone morphogenetic protein 2 L.MEHDNIARFIVGDER.F 1 2.454 0.061 receptor type ii precursor (ec 2 0 4

GP:AB002318_1 Human mRNA for KIAA0320 gene, 2 K.KLEQLKPR.A 2 2.954 0.092 partial cds. 2 3

GP:AB002344_1 Human mRNA for KIAA0346 gene, 2 R.PDLGGASKAKPP.T 1 2.124 0.119 partial cds. 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:Y12490_1 Homo sapiens mRNA for Golgi- 2 Q.VLQIEK.V 1 2.249 0.104 associated microtubule-binding 3 2 0.67

GP:Y11072_1 Homo sapiens mRNA for 2 E.KPKVTPNPDLLDLVQTADEKRRQR.D 2 2.349 0.055 synaptopodin; actin-associated 1 1

GP:U97276_1 Homo sapiens quiescin (Q6) 2 R.LDVPVWDVEATLNFLK.A 2 3.599 0.322 mRNA, complete cds, alternatively 0 3

GP:AB002370_1 Human mRNA for KIAA0372 gene, 2 E.RVVYQPGYPKSIASTARWYLLR.H 2 2.292 0.075 complete cds. 1 1

GP:AB023213_1 Homo sapiens mRNA for 2 K.DFTCNPLNSISEPK.V 2 2.183 0.071 KIAA0996 protein, complete cds. 0 2

GP:U96700_1 Mus musculus serine proteinase 2 L.LPDEGVDLSK.V 1 2.333 0.07 inhibitor 6 (SPI6) mRNA, complete 1 2 2.98

SW:ICE6_HUMAN caspase-6 precursor (ec 3 2 R.EMFDPAE.K 1 2.163 0.188

2 1

GP:AB046850_1 Homo sapiens mRNA for 2 G.IVPETFTLSNLPHFR.I 1 1.863 0.076 KIAA1630 protein, partial cds; 2 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:SYA_HUMAN alanyl-trna synthetase 2 K.TCFYAEQGGQIYDEGYLVKV.D 2 2.663 0.15

1 4

SW:AAK2_HUMAN 5'-amp-activated protein kinase, 2 P.SYDANVIDDEAVKEVCEK.F 2 3.056 0.157 catalytic alpha-2 chain (ec 2 1 1 YES

SW:PIG2_HUMAN 1-phosphatidylinositol-4,5- 2 R.HYCAIADAKLSFSDDIEQTM.E 2 2.457 0.05 bisphosphate phosphodiesterase 0 2

SW:AKA8_HUMAN a-kinase anchor protein 8 (a- 2 K.EDEDEDVKKRREKQRRRDR.T 2 2.263 0.132 kinase anchor protein 95 kda) 1 2

SW:ALFA_HUMAN fructose-bisphosphate aldolase a 2 K.ALSDHHIYLEGTLLKPNMVTPGHACT 2 3.515 0.235 (ec 4 3 0

SW:PLO3_HUMAN procollagen-lysine,2-oxoglutarate 2 D.RNRVRIR.N 2 2.324 0.07 5-dioxygenase 3 precursor (ec 1 0 2

SW:PRO1_HUMAN profilin i 2 K.TFVNITPAEVGVLVGK.D 1 3.917 0.377

4 4 0.85

SW:PYC_HUMAN pyruvate carboxylase precursor 2 D.VKGQIGAPMPGKVIDIKVVAGAKVAK.G 2 2.939 0.136 (ec 6 3 4 0.78 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:ANR3_HUMAN serine/threonine-protein kinase 2 K.HDVYSFAIV.I 1 2.057 0.169 ankrd3 (ec 2 0 4

SW:PYRD_HUMAN dihydroorotate dehydrogenase 2 K.EDIASVVKELGIDGLIVTNTTVSR.P 2 1.923 0.05 precursor (ec 1 1 1

SW:BU1B_HUMAN mitotic checkpoint 2 F.RKKLKEQR.E 1 2.606 0.098 serine/threonine-protein kinase 2 3 0.69

SW:RBL1_HUMAN retinoblastoma-like protein 1 (107 2 E.KEAVITPVASATQSVSR.L 2 2.607 0.127 kda retinoblastoma-associated 1 1

SW:SYEP_HUMAN bifunctional aminoacyl-trna 2 K.QYVNKNSKHEELMLGDPCLKDLKK. 3 3.214 0.106 synthetase [includes: glutamyl- 0 3

SW:SELW_HUMAN O15532 homo sapiens (human), 2 C.GEGTPQATGFFEVMVAGKLIHSKK.K 2 2.474 0.077 and macaca mulatta (rhesus 1 1

SW:2AAA_HUMAN serine/threonine protein 2 K.SALASVIMGLSPILGKDNTIE.H 2 2.280 0.111 phosphatase 2a, 65 kda 1 2

SW:CRP_HUMAN c-reactive protein precursor 2 K.RQDNEILIFWSK.D 2 3.986 0.329

0 4 YES YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:TELT_HUMAN telethonin (titin cap protein) 2 R.RSLSRSMSQEAQR.G 1 1.952 0.111

2 1

SW:CLH2_HUMAN clathrin heavy chain 2 (clh-22) 2 Q.IFNIEMK.S 1 2.025 0.059

4 4 1.6

SW:TPMS_HUMAN tropomyosin alpha chain, smooth 2 R.KYEEVAR.K 1 2.651 0.224 muscle (tropomyosin 1, smooth 4 7 0.67 YES

SW:CN4D_HUMAN camp-dependent 3',5'-cyclic 2 R.QGQTEKFQFELTLEE.D 1 2.511 0.065 phosphodiesterase 4d (ec 3 2 1

SW:VGR3_HUMAN vascular endothelial growth factor 2 R.FRAMVELAR.L 2 3.16 0.125 receptor 3 precursor (ec 2 2 0

SW:ZYX_HUMAN zyxin (zyxin 2) 2 K.EVEELEQLTQQLMQDMEHPQR.Q 2 3.876 0.367

4 6 0.47

GP:AB020653_1 Homo sapiens mRNA for 2 A.EHLTFLEHK.S 1 1.837 0.086 KIAA0846 protein, complete cds. 0 2

GP:AB010419_1 Homo sapiens mRNA for MTG8- 2 P.IDSSELLLEVNENGK.R 2 2.302 0.109 related protein MTG16a, complete 2 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF216648_1 Homo sapiens LPS responsive 2 R.SGITPKGLDGPRPNQK.E 2 2.455 0.13 and Beige-like anchor protein 0 5 YES

GP:D50857_1 Human DOCK180 protein mRNA, 2 K.HKYLAKTGETFVK.L 1 2.027 0.071 complete cds; 180-kDa protein 1 1

SW:RGSC_HUMAN regulator of g-protein signaling 12 2 K.SGRSLNEELGDEDSEKKRKG.A 2 3.054 0.138 (rgs12) 2 2 0.52

GP:BC000041_1 Homo sapiens, Similar to 2 K.QALWLTKTKLIEG.L 1 2.011 0.091 ribosomal protein, mitochondrial, 0 2

SWN:IP3R_HUMAN inositol 1,4,5-triphosphate 2 R.GEMSLAEVQC.H 1 2.411 0.086 receptor type 1 2 1

SW:IF4G_HUMAN eukaryotic translation initiation 2 R.LQGINCGPDFTPSFANLGRTTLSTR 3 3.324 0.104 factor 4 gamma (eif-4-gamma) 2 0

SW:IFR1_HUMAN interferon-related developmental 2 I.TELYSTLECLENIFTKSYLKEK.D 2 2.411 0.069 regulator 1 (nerve growth factor- 2 0

SW:IRE2_HUMAN iron-responsive element binding 2 R.EFNSYGARR.G 1 2.250 0.197 protein 2 (ire-bp 2) (iron 4 4 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:KC1D_HUMAN casein kinase i, delta isoform (ec 2 2 R.KIGSGSFGDIYLGTDIAAGEEVAIKLE 2 2.316 0.096

1 1

SW:KF5C_HUMAN kinesin heavy chain isoform 5c 2 K.SEVKSLVNR.S 2 2.484 0.071 (kinesin heavy chain neuron- 0 4

SW:KINN_HUMAN neuronal kinesin heavy chain 2 K.LEAELSRWR.N 2 2.547 0.064 (nkhc) (kinesin heavy chain 2 2 YES

SW:TIAM_HUMAN t-lymphoma invasion and 2 K.FLIENKM.Q 1 2.096 0.069 metastasis inducing protein 1 1 1

SW:LCFC_HUMAN long-chain-fatty-acid--coa ligase 2 A.KASMENQPHSK.P 1 2.022 0.089 3 (ec 6 1 1

SW:LYST_HUMAN lysosomal trafficking regulator 2 K.VADMLLDNGLLY.V 1 2.421 0.084 (beige homolog) 2 0

SW:M3K8_HUMAN mitogen-activated protein kinase 2 A.GEGGSVLEKLESCGPMR.E 2 2.251 0.095 kinase kinase 8 (ec 2 3 0

SW:PIB2_HUMAN 1-phosphatidylinositol-4,5- 2 L.ASPVASQVNGALAPTSNGSPAARAG 2 2.628 0.051 bisphosphate phosphodiesterase 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:MA2B_HUMAN lysosomal alpha-mannosidase 2 K.TVDQYFYGIKNDIQHAGVQYILD.S 2 2.284 0.219 precursor (ec 3 2 2 YES

SW:PGMU_HUMAN phosphoglucomutase (ec 5 2 R.SMPTSGALDR.V 1 1.887 0.252

1 1

GP:U53531_1 Human cytoplasmic dynein 2 2 K.NKVPLSNNVE.T 1 2.042 0.177 heavy chain mRNA, partial cds; 6 4 1.53 0.16

SW:MY15_HUMAN myosin xv (unconventional 2 N.QCIIISGESGSGKTEATK.L 1 2.800 0.086 myosin-15) 1 1

GPN:AL137068_2 Human DNA sequence from clone 2 K.SLKHHEDIVDEIECIEKTLLKRRSELR 2 2.645 0.057 RP11-165P4 on chromosome 2 0

SW:MYH4_HUMAN myosin heavy chain, skeletal 2 K.GGKKKGSSFQTVSALFR.E 2 1.934 0.329 muscle, fetal (myosin heavy chain 4 0

SW:MYHB_HUMAN myosin heavy chain, smooth 2 F.EQLCINYTNEK.L 2 2.435 0.053 muscle isoform (smmhc) 1 1

PIR2:I38025 keratin-like protein - human 2 D.NSRDLNMDCIIAEIK.A 2 2.698 0.102 (fragment) 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:MYHD_HUMAN myosin heavy chain, skeletal 2 A.ELGEQIDNLQR.V 1 1.906 0.066 muscle, extraocular (myhc-eo) 0 2 YES

SW:NS2A_HUMAN nitric oxide synthase, inducible 2 D.SQHKGVRGGRMTLVFGCR.R 2 2.326 0.055 (ec 1 1 1

SW:OM70_HUMAN mitochondrial precursor proteins 2 D.KVISLKEANVK.L 1 1.862 0.136 import receptor (translocase of 1 1

PIR2:T08745 probable RNA helicase - human 2 K.GKKLNIGGGGLGY.R 1 2.064 0.145

2 0

SW:PDA4_HUMAN protein disulfide isomerase a4 2 K.LKPVIKSQPVPKNNKGPVKVVVGKT 3 3.920 0.194 precursor (ec 5 0 3 YES

GP:AF338650_1 Homo sapiens PDZ domain- 2 K.MELLKESDGLGIQVSGGRGSKRSP 2 2.22 0.066 containing protein AIPC (AIPC) 2 3 7.79

SW:M3KE_HUMAN mitogen-activated protein kinase 2 K.IASEPPPVR.E 1 1.857 0.132 kinase kinase 14 (ec 2 7 2 0.89

GP:BC011808_1 Homo sapiens, Similar to 2 F.KGWPWLLPDGSPVDIFAKIK.A 2 2.738 0.084 hypothetical protein FLJ23316, 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC015932_1 Homo sapiens, clone MGC:8927 2 E.SSTEPNDSLWFSLQK.K 2 2.223 0.121 IMAGE:3909331, mRNA, complete 2 0

GP:BC015713_1 Homo sapiens, hypothetical 2 L.PVVEEGEVLSHSLEAEHRLLK.A 2 2.939 0.145 protein SP192, clone MGC:16819 1 4 0.83

GP:BC014331_1 Homo sapiens, hypothetical 2 A.AKPEDVYK.F 1 1.911 0.095 protein FLJ13390 similar to 5 9 2.44

GP:BC014320_1 Homo sapiens, clone MGC:22821 2 K.VDVIPVTAINLYPDGPE.K 1 1.958 0.117 IMAGE:3686673, mRNA, complete 2 0

GP:BC014077_1 Homo sapiens, clone MGC:20455 2 F.ESWHSLALAK.G 1 1.839 0.105 IMAGE:4126671, mRNA, complete 5 0

SW:PZP_HUMAN pregnancy zone protein precursor. 2 K.GHFSISIPVK.S 1 7.088 0.573

12 10 0.79 0.23 YES YES

GP:BC013650_1 Homo sapiens, clone MGC:17536 2 K.KVDGRAHGAIGADVDGGDLNF.G 2 2.796 0.132 IMAGE:3460756, mRNA, complete 2 1

GP:D86970_1 Human mRNA for KIAA0216 gene, 2 E.AGLLQLDVPLLRTQLRGSRLLDAMR 3 3.897 0.11 complete cds; similar to myosin 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC011414_1 Homo sapiens, clone MGC:16827 2 I.RSLAELTACSIELFHK.T 2 2.734 0.107 IMAGE:3855873, mRNA, complete 2 0

GP:BC010619_1 Homo sapiens, clone MGC:16799 2 L.RDRFWLVINQEGNMVTAR.Q 2 2.282 0.1 IMAGE:3872779, mRNA, complete 4 2 1.36

SW:AD28_HUMAN adam 28 precursor (ec 3.4.24.-) 2 C.ALGECCEKCQFK.K 2 2.518 0.139 (a disintegrin and 4 10 1.15

SW:AD08_HUMAN adam 8 precursor (ec 3 2 R.RHLHDNVQLITGV.D 1 1.859 0.082

0 3

PIR1:PLHU plasmin (EC 3.4.21.7) precursor 2 A.PPPVVLLPNVETPSEEDCMFGNGK. 2 5.118 0.274 [validated] - human 2 1 0.95

GP:AY028899_1 Homo sapiens ATP-binding 2 K.GEVIGLLGHNGAGK.S 2 2.696 0.082 cassette A9 mRNA, complete cds; 1 1

GP:BC014071_1 Homo sapiens, clone MGC:20569 2 I.SIPAVQKVFNRITDASALRLVDK.A 2 2.633 0.09 IMAGE:4024994, mRNA, complete 1 1

PIR2:T14756 hypothetical protein 2 K.LNEAIKLAK.G 2 4.224 0.278 DKFZp564F0923.1 - human 1 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:T46422 hypothetical protein 2 K.AKKSKTK.M 1 1.927 0.097 DKFZp434M2023.1 - human 1 1

PIR2:T46385 Homo sapiens, Similar to 2 R.LSQLDSCVHPVLAFPDDVPTSLH.F 2 3.991 0.126 DKFZP727C091 protein, clone 2 3

PIR2:T46354 hypothetical protein 2 K.EMVVCSSESITCKPQ.L 2 2.292 0.131 DKFZp434F1016.1 - human 2 0

PIR2:T42664 hypothetical protein 2 K.DPHGEKREFQDAPYNEVTGA.P 2 2.285 0.111 DKFZp434P1115.1 - human 1 1

PIR2:T42658 hypothetical protein 2 K.QLHQKLILAEAVME.G 2 2.453 0.07 DKFZp434K0115.1 - human 5 5 0.51

PIR2:T17269 hypothetical protein 2 P.REEVLPEK.E 1 2.087 0.072 DKFZp434N231.1 - human 2 2

GP:D79991_1 Homo sapiens mRNA for 2 F.YNELYK.H 1 2.056 0.058 KIAA0169 protein, partial cds; 1 3 1.58

PIR2:T17248 hypothetical protein 2 H.TFGGPLLK.T 1 2.426 0.066 DKFZp586G1122.1 - human 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:D80003_1 Human mRNA for KIAA0181 gene, 2 K.MVYQESPQNPSSSPLAEMASLPE.A 2 2.499 0.075 partial cds. 1 1

PIR2:T12545 hypothetical protein 2 K.EVPFDALTYLTGECNYGGRVTDD.K 2 2.494 0.131 DKFZp434N074.1 - human 1 1

PIR2:T02345 hypothetical protein KIAA0324 - 2 E.LDVKPSASPQERSESDSSPDSKAK 2 2.207 0.087 human (fragment) 1 1

PIR2:T00382 hypothetical protein KIAA0634 - 2 R.ESFRSSRLQTHNSVIGVPIR.E 2 2.358 0.094 human (fragment) 1 1

PIR2:T00380 KIAA0637 protein - human 2 P.QPADAGDLSTILSPIK.L 1 1.932 0.056

3 0

PIR2:T00344 hypothetical protein KIAA0586 - 2 A.ATAAAIATAAPLIK.V 1 2.046 0.062 human 0 3

PIR1:KGHUL1 kininogen, LMW precursor 2 K.EETTSHLR.S 1 4.136 0.343 [validated] - human 13 15 1.63 1.4 YES

PIR2:T17257 hypothetical protein 2 K.SVLEGGDIPLQGLSGLK.R 2 2.005 0.156 DKFZp586P1422.1 - human 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC002950_1 Homo sapiens, Similar to colon 2 R.AVILLSTTVLENVLQP.F 2 2.319 0.128 cancer-associated protein Mic1, 2 0

PIR2:I38228 Shb protein - human 2 K.QIWYHGAISR.G 2 2.007 0.128

3 1 1.65

PIR2:A41685 SIL protein - human 2 I.SPNNMSFATKK.Y 2 2.54 0.091

0 4

GPN:AF403030_1 Homo sapiens ankyrin repeat 2 R.DGAVAILQELLDHGAEANVKAKLPV. 2 3.047 0.168 domain-containing SOCS box 11 7 0.59

GPN:AF403027_1 Homo sapiens SPRY domain- 2 G.ERRAEPHSLLHLSR.L 1 2.313 0.052 containing SOCS box protein SSB- 0 3

GPN:AF073920_1 Homo sapiens regulator of G- 2 K.ARLELADYEAENLARLQRAFAKKWE 2 2.677 0.06 protein signaling 6 (RGS6) mRNA, 2 0

GP:J02619_1 Human Z type alpha-1-antitrypsin 2 K.DTEEEDFHVDQATTVK.V 1 5.093 0.48 gene, complete cds (exons 2-5); 28 15 1.27 0.42

GP:BC006404_1 Homo sapiens, suppressor of 2 G.YVGHEEGGQLTK.K 1 1.927 0.063 potassium transport defect 3, 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:S71752 giant protein p619 - human 2 K.ANKPISCLAYLSTAVGCLA.S 2 2.200 0.17

0 3

GP:BC001568_1 Homo sapiens, CDC5 (cell division 2 E.IDDTYIEDAADVDARKQAIR.D 2 2.533 0.079 cycle 5, S. pombe, homolog)-like, 1 1

GP:AY057448_1 Homo sapiens MARK4 2 E.AELKEER.L 1 1.923 0.068 serine/threonine protein kinase 0 6

GP:AY044449_1 Homo sapiens muscle alpha- 2 K.VRAAGDGEATTPEERESPTVSPRG 3 3.952 0.225 kinase (MAK) mRNA, complete 6 6 1.27

GP:AY037158_1 Homo sapiens pregnancy-induced 2 R.FVQGGA.L 1 1.835 0.108 growth inhibitor mRNA, complete 2 2

GP:AY033593_1 Homo sapiens prostein mRNA, 2 K.PGAPFPNGHVGAGGSGLLPPP.P 2 2.313 0.137 complete cds. 2 3

GP:AY033486_1 Homo sapiens ATP-binding 2 R.SLKQMHLPRSVPLTQAMYR.S 2 1.985 0.091 cassette transporter family A 0 3

GP:Z30326_1 S.cerevisiae genes for ubiquitin 2 R.QFLFRQKDIKQPK.S 2 2.488 0.103 activating enzyme-like protein and 5 3 0.65 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:TRFL_HUMAN lactotransferrin precursor 2 H.YYAVAVVK.K 1 1.960 0.339 (lactoferrin) [contains: 6 4 0.95 YES

GP:U28494_1 Mustela putorius fibrinogen 2 S.NIRFLQEIYNSNNQK.I 2 3.082 0.108 gamma A chain mRNA, partial cds; 1 2 2.29 YES

SW:PRTC_HUMAN vitamin-k dependent protein c 2 K.STTDNDIALLHLAQPATLSQTIVPICL 2 5.063 0.374 precursor (ec 3 3 0 YES YES

SW:FHR2_HUMAN complement factor h-related 2 R.LCFFPFVENGHSESSGQTHLEGDT 1 4.525 0.337 protein 2 precursor (fhr-2) (h 3 2 YES

SW:C1QC_HUMAN complement c1q subcomponent, 2 R.FNAVLTNPQGDYDTSTGK.F 1 4.796 0.452 c chain precursor 13 10 1.12 0.14 YES

SW:C1QB_HUMAN complement c1q subcomponent, 2 R.FDHVITNMNNNYEPR.S 1 4.902 0.398 b chain precursor 14 10 0.68 0.11 YES

SW:BAN7_HUMAN erythrocyte band 7 integral 2 K.NSTIVFPLPIDMLQGIIGAK.H 2 3.405 0.32 membrane protein (stomatin) 5 0

PIR2:I52300 giantin - human 2 D.RVIDEAKKWER.K 1 2.081 0.061

1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:U24578_2 Human RP1 and complement C4B 2 R.STQDTVIALDALSAYWFASHTTEER.G 2 3.761 0.326 precursor (C4B) genes, partial 4 2 1.21 0.26

PIR2:JC5290 protein-tyrosine-phosphatase (EC 2 A.TVLEMIRCHNLVDVFFAAKTLR.N 3 3.869 0.116 3.1.3.48) - human 0 3 YES

SW:PLE1_HUMAN plectin - human 2 R.DPYSGSTISL.F 1 1.892 0.089

0 2 YES

SW:PHL2_HUMAN phosphatidylinositol-glycan- 2 R.FGGVLHLSDLDDDGLDEIIMAAPLR.I 2 6.261 0.549 specific phospholipase d 2 2 6 1.34 YES

SW:BIG2_HUMAN brefeldin a-inhibited guanine 2 I.SQEHEGDLDLHTNDVDK.S 2 2.302 0.059 nucleotide-exchange protein 2 2 1

SW:APXL_HUMAN apical-like protein (apxl protein) 2 R.YSEESTPADLGPRAQSPGSPLHAR.G 2 2.291 0.182

0 2

PIR2:T03455 ALR protein - human 2 K.ASPVPSDPEK.P 2 1.956 0.106

0 3

SW:RGL1_HUMAN ral guanine nucleotide 2 R.CGRSGPGPGRGAAGLSP.A 2 2.414 0.17 dissociation stimulator-like 1 2 2 0.29 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

PIR2:S27041 complement component C3b - 2 A.GAKDQLTCNK.F 1 2.667 0.103 human (fragments) 1 1

GP:AK056522_1 Homo sapiens cDNA FLJ31960 fis, 2 A.YRSLANFSAGEHTILHLPEK.I 2 2.527 0.105 clone NT2RP7007504; unnamed 3 0

GP:AL136668_1 Homo sapiens mRNA; cDNA 2 K.KLYSSEQLPIEE.C 2 3.317 0.094 DKFZp564O2071 (from clone 5 2 1.05

GP:AF207881_1 Homo sapiens tumor-associated 2 R.RLVNEKAAHEK.D 2 2.749 0.239 hydroquinone (NADH) oxidase 8 21 1.95

GP:AK058027_1 Homo sapiens cDNA FLJ25298 fis, 2 K.SAVQGPPDRDLCGCYSVSSVLPGC 2 4.350 0.274 clone STM07683, highly similar to 5 2 0.35

GP:AK057694_1 Homo sapiens cDNA FLJ33132 fis, 2 E.DMLEDEEEEDDK.D 1 2.008 0.121 clone UMVEN2000133, weakly 2 2

GP:AK057217_1 Homo sapiens cDNA FLJ32655 fis, 2 K.TFMGKAQNQKYQ.G 2 2.426 0.062 clone TESTI1000025, weakly 3 3 1.5

PIR2:T46936 hypothetical protein 2 K.ESVLQFYPKANIVAYHDSIMNPDYN.V 2 2.232 0.066 DKFZp434H239.1 - human 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK056591_1 Homo sapiens cDNA FLJ32029 fis, 2 R.KEDNGYK.V 2 2.086 0.11 clone NTONG1000264; unnamed 0 3

GP:AY007123_1 Homo sapiens clone CDABP0017 2 R.DVAKMLPTLGGEEGVSR.I 2 1.931 0.074 mRNA sequence; similar to Homo 2 1

GP:AK055545_1 Homo sapiens cDNA FLJ30983 fis, 2 G.CPMRSRHLLQLLSNSHR.L 2 2.296 0.238 clone HHDPC2000455, weakly 0 2

GP:AK055204_1 Homo sapiens cDNA FLJ30642 fis, 2 R.KMIKEARK.V 1 1.962 0.079 clone CTONG2002965; unnamed 0 2

GP:AK027386_1 Homo sapiens cDNA FLJ14480 fis, 2 K.LLAVQELLDREALEK.F 1 2.406 0.079 clone MAMMA1002215; unnamed 2 2

GP:AK023197_1 Homo sapiens cDNA FLJ13135 fis, 2 L.LESSLISLSR.Y 1 1.844 0.068 clone NT2RP3003078, highly 0 6

GP:AK023105_1 Homo sapiens mRNA for 2 G.DGPGVPAQASDHGLPPPDISVVSVIV 2 2.521 0.075 KIAA1441 protein, partial cds; 1 1

GP:AK022451_1 Homo sapiens cDNA FLJ12389 fis, 2 E.SFEEVEDSLCVPQYNKYR.E 2 2.479 0.089 clone MAMMA1002671, weakly 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK057204_1 Homo sapiens cDNA FLJ32642 fis, 2 K.QIITDKDDLVK.S 1 2.212 0.084 clone SYNOV2001144; unnamed 2 0

GP:BC007227_1 Homo sapiens, clone 2 H.SPVAGVAHR.F 1 1.823 0.191 IMAGE:2963841, mRNA, partial 2 2

PIR2:T00076 hypothetical protein KIAA0462 - 2 R.RQVRKLLLFICGSKEKYR.Q 2 2.526 0.142 human (fragment) 1 2

PIR2:T00069 hypothetical protein KIAA0454 - 2 S.SASSTPGSETPIINR.A 1 1.850 0.112 human (fragment) 4 1

GPN:BC019901_1 Homo sapiens, clone MGC:29981 2 R.YYCFQGNKFLR.F 1 3.192 0.295 IMAGE:5123914, mRNA, complete 5 2 0.31

GP:BC018661_1 Homo sapiens, clone 2 K.RHENNLSVLAISNMEASSTLAKC.L 2 2.683 0.194 IMAGE:4105114, mRNA, partial 0 3

GP:BC017592_1 Homo sapiens, clone MGC:27006 2 F.GVPLAPEGIR.G 2 2.363 0.06 IMAGE:4828408, mRNA, complete 2 0

GP:BC016918_1 Homo sapiens, hypothetical 2 P.HRVAFVEK.L 1 1.959 0.115 protein FLJ11026, clone 3 2 0.97 0.18 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AL136749_1 Homo sapiens mRNA; cDNA 2 K.AYVVEDSKQLILEGQH.H 2 2.211 0.06 DKFZp434D0814 (from clone 2 1

GP:BC008315_1 Homo sapiens, clone 2 K.AETEQHIKVPASMTAEE.L 2 2.602 0.058 IMAGE:3161752, mRNA, partial 10 5 1.32

GP:AL136932_1 Homo sapiens mRNA; cDNA 2 R.NHFDRSVVLNDVFLSKETKHML.K 2 2.331 0.072 DKFZp586H1322 (from clone 0 2

GP:BC006135_1 Homo sapiens, Similar to RIKEN 2 R.QVEELQQRIQAGEV.S 1 2.582 0.169 cDNA A030010B05 gene, clone 2 0

GP:BC003404_1 Homo sapiens, hypothetical 2 K.ESLLLEDSEEE.E 1 1.859 0.083 protein DKFZp586F1122 similar to 2 0

GP:BC002575_1 Homo sapiens, clone 2 E.PRRVAAVAMSQR.V 1 2.354 0.059 IMAGE:3161568, mRNA, partial 1 1

GP:BC001099_1 Homo sapiens, clone 2 R.VQLLDYVISSF.Y 1 2.133 0.105 IMAGE:3510317, mRNA, partial 2 4 0.91

GP:BC000552_1 Homo sapiens, clone MGC:3020 2 R.PSQETTPPDRSHHSGFGLFCGD.P 2 3.249 0.114 IMAGE:3162851, mRNA, complete 3 2 0.73 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK000143_1 Homo sapiens cDNA FLJ20136 fis, 2 E.GSDLLENHIKK.L 1 2.076 0.122 clone COL07068; unnamed 7 1 9.14

GP:BC009379_1 Homo sapiens, Similar to RIKEN 2 K.YLVMDEADRIL.N 1 2.017 0.082 cDNA 4930588A18 gene, clone 1 1

SW:HGFL_HUMAN hepatocyte growth factor-like 2 R.GTELQHLLHAVVPGPWQEDVADAE 2 4.597 0.147 protein precursor (macrophage 2 3 1.06 0.63 YES

GP:AK000913_1 Homo sapiens cDNA FLJ10051 fis, 2 K.KTKQTLKEVQ.T 1 1.994 0.119 clone HEMBA1001281; unnamed 1 2

GP:AB033035_1 Homo sapiens mRNA for 2 K.RLILENHAAKIPAKAKQA.I 2 2.488 0.059 KIAA1209 protein, partial cds; 3 0

GP:AB033027_1 Homo sapiens mRNA for 2 K.LYDLLFTNSPFQRDFMEQRR.F 2 2.614 0.073 KIAA1201 protein, partial cds; 2 1 0.91

GP:AB032957_1 Homo sapiens mRNA for 2 L.ERAPGETALIDRTGR.M 1 2.441 0.12 KIAA1131 protein, partial cds; 0 3

GP:AB029033_1 Homo sapiens mRNA for 2 H.NSGLGAER.G 2 2.372 0.114 KIAA1110 protein, partial cds; 0 3 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB023226_1 Homo sapiens mRNA for 2 R.SAPPLLKR.K 2 1.908 0.117 KIAA1009 protein, complete cds; 1 7 2.9

GP:AB037743_1 Homo sapiens mRNA for 2 K.NLDFEPLSTTALILE.D 1 2.485 0.069 KIAA1322 protein, partial cds; 3 0

SW:MPRI_HUMAN cation-independent mannose-6- 2 K.SVKALSSLHGDDQDSEDEVLTIPE.V 2 3.053 0.077 phosphate receptor precursor (ci 0 2

GP:AB040883_1 Homo sapiens mRNA for 2 K.EANRRPEQG.S 2 2.208 0.103 KIAA1450 protein, partial cds; 1 2

SW:S109_HUMAN calgranulin b (migration inhibitory 2 R.NIETIINTFHQYSVK.L 2 4.270 0.441 factor-related protein 14) (mrp-14) 2 6 1.78

SW:Y226_HUMAN hypothetical protein kiaa0226 2 G.ELGPRLAELTRAGATHVER.C 2 2.536 0.087 (fragment) 1 1

SW:Y192_HUMAN hypothetical protein kiaa0192 2 D.FSNSLDSLCNR.I 1 2.051 0.167 (fragment) 1 1

SW:Y136_HUMAN hypothetical protein kiaa0136 2 H.QSTETDAVFLLESINGK.S 1 2.896 0.279 (fragment) 3 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:Y052_HUMAN hypothetical protein kiaa0052 2 R.LGFATSSDVIEMKGRVAC.E 2 2.581 0.054 (fragment) 1 1

SW:C1QA_HUMAN complement c1q subcomponent, 2 R.SLGFCDTTNK.G 1 2.312 0.358 a chain precursor 10 4 0.57 YES

SW:AVR2_HUMAN activin receptor type ii precursor 2 R.GTSVDVDLWLITAFHEKGSLSDFLK.A 2 2.217 0.178 (ec 2 0 2

GP:AB058765_1 Homo sapiens mRNA for 2 P.CPGGTPAGSSGGSPGEDPRR.T 1 1.960 0.156 KIAA1862 protein, partial cds; 2 0

SW:IF2M_HUMAN translation initiation factor if-2, 2 E.RPAALPSASPPPR.E 1 1.948 0.057 mitochondrial precursor (if-2mt) 1 2

GP:AF284014_1 Sus scrofa BRCA1 gene, partial 2 K.RSPSPLAHR.R 1 1.965 0.131 cds; similar to Homo sapiens 3 2

GP:AF040965_1 Homo sapiens unknown protein 2 R.ALRKRTQTLLKEYKER.D 2 2.131 0.078 IT12 mRNA, partial cds; similar to 0 2

GP:AE006466_2 Homo sapiens 16p13.3 sequence 2 R.GPLGLVGAAAKGE.L 1 2.030 0.086 section 5 of 8; Structure of CDS 3 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AC007228_1 Homo sapiens chromosome 19, 2 G.LVTIKNLAVDFRQQLHPAQK.N 2 2.566 0.074 BAC 37295 (CIT-B-21A4), 1 1

GP:AC004886_1 Homo sapiens PAC clone RP4- 2 R.EPYDSVEESSESENSPVPQRKR.R 2 2.258 0.13 784G16 from 7q11.23-q21.1, 0 3

GP:AB037728_1 Homo sapiens mRNA for 2 R.EEALQADKK.L 1 1.945 0.07 KIAA1307 protein, partial cds; 1 2

GP:AB067468_1 Homo sapiens mRNA for 2 A.VSTGLTGAVNVARGSIQTGVDTSK.T 2 3.032 0.089 KIAA1881 protein, partial cds; 4 0

GP:AK000800_1 Homo sapiens cDNA FLJ20793 fis, 2 K.MDATSYSSIASEFGVRGYPTIK.L 2 1.906 0.155 clone COL00343; unnamed 3 0

GP:AB058761_1 Homo sapiens mRNA for 2 K.GSATKPAGCQSSSKDRSAAS.T 1 1.893 0.127 KIAA1858 protein, partial cds; 0 3

GP:AB058686_1 Homo sapiens mRNA for 2 K.QGPLLDLFGQK.L 1 1.988 0.058 KIAA1783 protein, partial cds; 0 4

GP:AB051517_1 Homo sapiens mRNA for 2 E.ALFHLFSLTHVMEKTK.P 1 2.392 0.063 KIAA1730 protein, partial cds; 0 2 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB051485_1 Homo sapiens mRNA for 2 K.LVAAAPPAL.C 1 1.87 0.117 KIAA1698 protein, partial cds; 1 1

GP:AB046802_1 Homo sapiens mRNA for 2 A.AKPLGCRPPISKESSVDR.P 2 2.633 0.188 KIAA1582 protein, partial cds; 0 3

GP:AB040936_1 Homo sapiens mRNA for 2 D.YNKFRAGIK.D 1 2.021 0.05 KIAA1503 protein, partial cds; 3 0

GP:AC004155_1 Mus musculus DNA from BAC 2 R.DYLSAGA.E 1 1.911 0.081 10818 containing the Ercc-4 gene, 1 1

GP:AF070645_1 Homo sapiens clone 24650 2 E.RSHSARMTLAKACELCPEEVK.K 2 2.991 0.102 ubiquitin hydrolase mRNA, partial 1 1

GP:AF257305_1 Homo sapiens ASH1 mRNA, 2 R.KMCNYDKILATKKNLDHVNKILKAK.K 2 2.807 0.064 complete cds; huASH1. 2 0

GP:AB017802_1 Homo sapiens mRNA for clg01, 2 L.SLLKLLKSSNRR.I 2 2.521 0.09 complete cds. 2 2

GP:AB018551_1 Homo sapiens ATPBL mRNA for 2 A.KLGKTRLKPTMPAAAPIPQPAGR.H 2 2.454 0.07 coiled-coil protein, complete cds. 0 4 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:NKC1_HUMAN bumetanide-sensitive sodium- 2 G.DFVIGTFIPLESKK.P 1 3.111 0.271 (potassium)-chloride cotransporter 11 8 1.01

SW:NEO1_HUMAN neogenin precursor 2 R.NSQDITPVDNSMDSNIHQRRNSYR. 1 2.316 0.147

0 3

GP:AB033107_1 Homo sapiens mRNA for 2 K.EGKETGSPKMDAK.L 1 2.366 0.06 KIAA1281 protein, partial cds; 1 1

GP:AB035898_1 Homo sapiens hklp2 mRNA for 2 L.KKENVRLAEETEK.L 1 1.875 0.094 kinesin-like protein 2, complete 3 1

GP:AB040955_1 Homo sapiens mRNA for 2 K.HLSVGPGQGPGSAVDEHQDNVFFP.S 2 2.686 0.084 KIAA1522 protein, partial cds; 3 0

GP:AC004912_2 Homo sapiens PAC clone RP5- 2 P.PPPPPPTPPPLPPASVLSDKAVK.P 2 2.478 0.136 871B15 from 7p15.3-7p14, SH3 2 2

GP:AF000981_1 Homo sapiens testis-specific 2 K.AAFPPRKTQNDQ.R 1 1.867 0.127 ChromoDomain Y isoform 1 0 2

SW:MRP2_HUMAN canalicular multispecific organic 2 E.LGPSVLAGVGVMVLVIPINAILSTKSK. 2 2.238 0.072 anion transporter 1 (multidrug 1 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SWN:FXP2_HUMAN forkhead box protein p2 (cag 2 K.KQQEQLHLQLLQQ.Q 2 3.471 0.108 repeat protein 44) 4 3 1.2 0.99

GP:AF020043_1 Homo sapiens chromosome- 2 C.RSMEVSTQLAR.A 1 2.403 0.134 associated polypeptide (HCAP) 3 2 0.99

SW:OAT6_HUMAN liver-specific organic anion 2 R.VSSLVLYIILIYAMK.K 2 2.648 0.082 transporter (organic anion 3 0

GP:AF098162_1 Homo sapiens timeless homolog 2 H.HLVQMGLADSVKDFQR.K 2 3.654 0.278 mRNA, complete cds; hTIM. 2 4 1.14 0.14

GP:AF132743_1 Oryza sativa 3-phosphoinositide- 2 K.LAMEANANEDEDSQ.D 1 2.348 0.109 dependent protein kinase-1 0 2

GP:AF151691_1 Mus musculus DNA polymerase 2 K.LGTGNHDSMPPL.I 1 1.878 0.217 iota (PolI) mRNA, complete cds; 0 3

GP:AF152516_1 Homo sapiens protocadherin 2 S.QEFSLTADSRK.S 1 2.089 0.161 gamma A9 short form protein 0 2

SW:MEPB_HUMAN meprin a beta-subunit precursor 2 K.GDDVYILLTVEDISHLNSTQ.I 2 2.352 0.069 (ec 3.4.24.18) (endopeptidase-2) 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF156271_1 Homo sapiens RING finger protein 2 L.QLEERSTQGPLQMLQDMKEPLSRK 2 2.572 0.051 terf mRNA, complete cds; RING 0 2

GP:AF175723_1 Porphyromonas gingivalis strain 2 L.TASYQSETNSGLGYDK.N 1 2.606 0.085 W50 immunoreactive 61kD 0 7

SW:MDR1_HUMAN multidrug resistance protein 1 (p- 2 K.EVKILKGLNLK.V 2 2.630 0.057 glycoprotein 1) 2 0

SW:ITB4_HUMAN integrin beta-4 precursor (gp150) 2 D.SSNIVELLEEAFNR.I 1 2.182 0.127 (cd104) 2 1 1.25

GP:AF245517_1 Homo sapiens vacuolar proton 2 L.EDEMQNEIVVQLLEK.S 1 2.858 0.076 pump 116 kDa accessory subunit 4 0

SW:ITAX_HUMAN integrin alpha-x precursor 2 A.RGQVLLLR.T 2 2.298 0.056 (leukocyte adhesion glycoprotein 2 6 0.57 YES

GP:AF016903_1 Homo sapiens agrin precursor 2 A.VPVEPGQWHRLELSRHWR.R 2 2.701 0.092 mRNA, partial cds. 0 2

SW:SIP1_HUMAN zinc finger homeobox protein 1b 2 K.KTESGMYACDLCDKTFQKSSSLLR 3 3.269 0.086 (smad interacting protein 1) 0 4 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:CENF_HUMAN cenp-f kinetochore protein 2 R.VRIEADEKKQLHIAEK.L 2 2.841 0.085 (centromere protein f) (mitosin) 2 2 YES

SW:DD21_HUMAN nucleolar rna helicase ii 2 G.RTIIFCETKK.E 2 2.228 0.062 (nucleolar rna helicase gu) (rh 2 0

SW:C2TA_HUMAN mhc class ii transactivator ciita 2 L.ARVLPDMVSLRVMDVQYNK.F 2 2.261 0.052

1 1

SW:BS4_HUMAN bs4 protein (ny-ren-18 antigen) 2 I.ALPCLLDADK.Y 1 1.810 0.144

2 1

PIR2:T00082 hypothetical protein KIAA0517 - 2 H.IIVVDNK.S 1 1.965 0.145 human (fragment) 1 2 2.27

SW:BASO_HUMAN zinc finger protein basonuclin 2 K.GQPAFPNIGQNGVLFPNLKTVQPV.L 3 3.910 0.079

1 1

SW:DDX7_HUMAN atp-dependent helicase ddx7 2 K.KRLKASKDKGKPKW.A 1 2.259 0.143 (dead-box protein 7) (np-52) 2 2

SW:DNM1_HUMAN dna (cytosine-5)- 2 R.EARAGVQADEDEDGDEKDEKKHR.S 2 2.952 0.075 methyltransferase 1 (ec 2 2 5 1.49 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:DPOA_HUMAN dna polymerase alpha catalytic 2 Q.YYLAQQIHPVVAR.I 1 2.046 0.11 subunit (ec 2 2 0

SW:DPOZ_HUMAN dna polymerase zeta catalytic 2 N.KRNQTNKLVDDGKK.K 1 2.249 0.116 subunit (ec 2 3 0

PIR2:I38414 transcription factor IIIC, box B- 2 K.VCLAEVYQDKALV.G 2 2.558 0.156 binding chain - human 3 3 0.29 0.16

SWN:RUN2_HUMA runt-related transcription factor 2 2 A.TSDFCLWPSTLSK.K 2 2.968 0.27 N (core-binding factor, alpha 1 6 3 1.05

GP:U94832_1 Human KH type splicing regulatory 2 A.FVEISRQLPPNGDPNFK.L 2 2.538 0.071 protein KSRP mRNA, complete 2 0

GP:AF155135_1 Homo sapiens novel retinal 2 G.HSALHLAAKNSHHECIRK.L 2 2.251 0.082 pigment epithelial cell protein 2 0

SW:SX13_HUMAN sox-13 protein (type 1 diabetes 2 K.EVVPAIEKLLSSD.W 1 2.871 0.118 autoantigen ica12) (islet cell 1 2

GP:AK027866_1 Homo sapiens cDNA FLJ14960 fis, 2 P.PSLTMPAEAK.T 1 1.898 0.063 clone PLACE4000192, weakly 2 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF332192_1 Homo sapiens transcription factor 2 P.EYTGLSTTGNGK.S 1 2.401 0.191 NYD-sp10 mRNA, complete cds. 1 4

GP:AY028898_1 Homo sapiens ATP-binding 2 E.DFIKSLK.H 1 1.899 0.099 cassette A6 mRNA, complete cds; 1 1

SW:WDR3_HUMAN wd-repeat protein 3 2 P.DQRGFVTGGADKSVK.F 1 2.338 0.12

4 4 1.29

SW:XPB_HUMAN tfiih basal transcription factor 2 E.AFSPVYKYAQDFLVAIAEPVCR.P 2 2.362 0.101 complex helicase xpb subunit (ec 1 1

SW:Z136_HUMAN zinc finger protein 136 2 E.KLYDCKECGKTFFSLK.R 2 2.93 0.109

0 2

SW:Z142_HUMAN zinc finger protein 142 (ha4654) 2 K.EHLKSH.T 1 1.864 0.069

1 1

SW:Z219_HUMAN zinc finger protein 219 2 E.AEPLDLSLR.A 1 2.261 0.155

3 5 0.81

SW:OXYR_HUMAN oxytocin receptor (ot-r) 2 I.VLATCYGLISFKIWQNLRLK.T 2 2.259 0.066

3 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:Z295_HUMAN zinc finger protein 295 2 G.NVLCALSQK.S 2 2.691 0.05

0 2

SW:ELF1_HUMAN ets-related transcription factor elf- 2 K.DLIYINDE.D 1 2.132 0.057 1 (e74-like factor 1) 0 4

GP:AF448144_1 Homo sapiens TruB pseudouridine 2 K.EKLLAEAG.M 1 2.314 0.145 synthase-like protein 1 (TRUB1) 1 5

GP:AJ404614_1 Homo sapiens mRNA for B-cell 2 R.CDICQMPFSVYSTLE.K 2 2.721 0.188 lymphoma/leukaemia 11B 0 2

GP:AF327442_1 Homo sapiens ciliary dynein heavy 2 K.LVDIQIMCAMGPPGGGRNPVTPR.Y 2 2.013 0.214 chain 7 (DNAH7) mRNA, complete 0 2

GP:AL022318_9 Human DNA sequence from clone 2 G.PSRPPLDAK.I 1 1.902 0.071 CTA-150C2 on chromosome 0 3

SW:GLR2_HUMAN glutamate receptor 2 precursor 2 S.AEDLSK.Q 1 1.915 1 (glur-2) (glur-b) (glur-k2) 1 1 YES

SW:GBR1_HUMAN gamma-aminobutyric acid type b 2 S.YITLVVLFVPK.M 1 2.409 0.08 receptor, subunit 1 precursor 2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF359281_1 Homo sapiens Bardet-Biedl 2 P.QSADNLK.Q 1 2.056 0.106 syndrome type 4 mRNA, complete 2 0

SW:GML_HUMAN glycosyl-phosphatidylinositol- 2 A.AEQPPEAPGKIFK.T 1 2.311 0.107 anchored molecule-like protein 1 1

GP:AF411132_1 Homo sapiens MRIP2 (MRIP2) 2 K.KRNGGGSLNNYSSSIPSTPSTSQED 2 2.383 0.079 mRNA, complete cds; ARF 2 1 1.53

GP:AF326730_1 Mus musculus HEC mRNA, 2 E.DLLENIR.E 1 1.917 0.1 complete cds; similar to Homo 5 2 1.35

SW:EPA5_HUMAN ephrin type-a receptor 5 2 E.EKMHFHNGHIK.L 1 1.884 0.1 precursor (ec 2.7.1.112) (tyrosine- 1 2

GP:AJ007421_1 Homo sapiens SALL3 gene, exons 2 R.LSNDSSSAVGDLESRSAGSPAL.S 2 2.528 0.083 1a, 2 and 3. 0 4

GP:AL049650_6 Human DNA sequence from clone 2 R.VNLSGATILYT.R 1 1.916 0.082 RP4-734P14 on chromosome 20. 2 1

SW:ITA7_HUMAN integrin alpha-7 precursor 2 Q.WLGVSVR.S 1 1.896 0.05

2 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:EG5_HUMAN kinesin-related motor protein eg5 2 K.LIAQNLELNETIK.I 1 2.230 0.052 (kinesin-like spindle protein hksp) 2 0

GP:AL031177_4 Human DNA sequence from clone 2 K.EQPKEYQRILQ.C 1 1.839 0.076 889N15 on chromosome Xq22.1- 1 1

SW:DESP_HUMAN desmoplakin (dp) (250/210 kda 2 R.EMRQMGQPCDAYQK.R 1 2.641 0.141 paraneoplastic pemphigus antigen) 1 3

GP:AL118520_3 Human DNA sequence from clone 2 K.KQKLLLELDQYAPD.V 2 2.217 0.064 RP11-346K17 on chromosome 20 0 5

GP:AL157713_2 Human DNA sequence from clone 2 P.VSSRNAIGGGGIGHQK.R 1 2.271 0.167 RP11-110J1 on chromosome 1 4 0.38

SW:CD14_HUMAN monocyte differentiation antigen 2 K.VLSIAQAHSPAFSCEQVR.A 2 3.491 0.42 cd14 precursor (lps receptor) (lps- 2 1 YES YES

SW:IRR_HUMAN insulin receptor-related protein 2 R.DLFPNLAVIRGTRLFLGYA.L 2 2.643 0.196 precursor (ec 2 3 5 2.43

GP:AY014957_1 Homo sapiens PI-3-kinase-related 2 R.LDKRDQSTIPRNL.L 1 2.058 0.185 kinase SMG-1 (SMG1) mRNA, 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AY014404_1 Homo sapiens kinesin-like protein 2 K.ANTLVREANFLAEEMSKLTDYQ.V 2 2.255 0.158 RBKIN2 (RBKIN) mRNA, complete 2 2

GP:AX173175_1 Sequence 1 from Patent 2 L.VIKLEK.V 1 2.249 0.089 WO0142295; human CLASP-7. 1 2 8.16

SW:CYGF_HUMAN retinal guanylyl cyclase 2 2 R.RRINKIQLIKGPNR.I 2 2.459 0.11 precursor (ec 4.6.1.2) (guanylate 2 0

GP:AL139395_1 Human DNA sequence from clone 2 E.KPALNK.P 1 1.890 0.088 RP11-130N24 on chromosome 2 4 1.12

SW:HXK2_HUMAN hexokinase, type ii (ec 2 2 R.GKFNTSDVSAIEKNK.E 1 1.988 0.067

3 0

GP:AF284018_1 Felis catus BRCA1 gene, partial 2 E.VYEQSLPISNCKCPEMKR.Q 2 2.853 0.054 cds; similar to Homo sapiens 1 1

GP:AL136805_1 Homo sapiens mRNA; cDNA 2 K.MVTSSPEEDLGTSY.Q 1 2.69 0.08 DKFZp434J1521 (from clone 3 2

GP:AL133353_1 Human DNA sequence from clone 2 D.HEDESDAEATQELAAGRRR.T 2 2.697 0.101 RP11-483F11 on chromosome 10 6 4 1.17 0.62 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:HSBX_HUMAN heat-shock 20 kda like-protein 1 A.VTSALSPEGVLSIQAAPASAQAPPPA 2 2.330 0.102 p20 0 2

GP:BC018730_1 Homo sapiens, hypothetical 1 C.QAEAAAAANGTGGEEDDGPAAELLE 2 4.141 0.163 protein FLJ20718, clone 2 0

SW:CAP1_HUMAN adenylyl cyclase-associated 1 K.AGAAPYVQAFDSLLAGPVAEYLK.I 2 3.119 0.361 protein 1 (cap 1) 2 0

GPN:AF327355_1 Homo sapiens hypothetical protein 1 K.RKKKKLLREQRK.Q 1 2.487 0.221 SB92 mRNA, complete cds. 2 0

SW:FHR1_HUMAN complement factor h-related 1 R.STDTSCVNPPTVQNAYIVSR.Q 2 3.885 0.352 protein 1 precursor (fhr-1) (h 2 1 0.77 YES

GPN:BC020256_1 Homo sapiens, clone MGC:32071 1 P.MPKKLFGSQLK.T 2 3.109 0.106 IMAGE:4870106, mRNA, complete 2 4 0.92

SW:DHB7_HUMAN estradiol 17 beta-dehydrogenase 1 L.DCIYLNAGIMPNPQLNIK.A 2 3.474 0.155 7 (ec 1 1 0

GP:AF155656_1 Homo sapiens zinc finger protein 1 K.KYECHKCLK.G 1 2.046 0.149 ZNF140-like protein mRNA, 0 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AK000990_1 Homo sapiens cDNA FLJ10128 fis, 1 Q.TLQKEIEKVYLDNKLLK.E 2 3.536 0.116 clone HEMBA1002997, weakly 4 2 0.63

GP:AK000361_1 Homo sapiens cDNA FLJ20354 fis, 1 K.RGVVILQNKSDDLPHWVLSAMKC.L 2 3.093 0.199 clone HEP15013; unnamed 6 2 1.54

GP:AB040900_1 Homo sapiens mRNA for 1 D.LVVLAIGELQPDLCFLLVSGR.T 2 3.722 0.156 KIAA1467 protein, partial cds; 2 0

GP:AC006794_2 Caenorhabditis elegans cosmid 1 T.SPFREFNNEYNPVIKFSKIR.F 2 3.997 0.151 Y50D4A, complete sequence; 2 2 0.9

GP:BC019041_1 Homo sapiens, Similar to 1 R.IHLMAGR.V 1 2.408 0.246 hypothetical protein HT036, clone 13 5 0.71 YES

GP:U79751_1 Human basic-leucine zipper 1 R.FHPYTRYENITFNCCNHC.R 2 3.147 0.227 nuclear factor (JEM-1) mRNA, 15 8

PIR2:I54383 chromosome segregation protein 1 F.NACFESVATNIDEIYKALSR.N 2 3.174 0.196 smc1 [similarity] - human 13 4 0.45

SW:ZF38_HUMAN zinc finger protein zfp-38 (ny-ren- 1 R.THTGEKPYVCTK.C 1 2.109 0.185 21 antigen) (fragment) 1 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AL138688_2 Human DNA sequence from clone 1 P.GAPPPAADFKLLALTEARGK.G 2 3.123 0.177 RP11-264J4 on chromosome 13. 0 2

GP:U53532_1 Human cytoplasmic dynein 3 1 Q.TRTTLGALVTIDVR.A 2 3.086 0.118 heavy chain mRNA, partial cds; 0 2

GPN:AF289614_1 Homo sapiens clone pp9949 1 R.SGPEPRPLGAAGDGQK.S 1 2.476 0.153 unknown mRNA. 2 0

SW:ILK2_HUMAN integrin-linked protein kinase 2 1 R.GDDTPLHLAASHGHR.D 2 3.927 0.467 (ec 2 4 2

SW:CA1C_HUMAN collagen alpha 1(xii) 1 T.MTGDAIDYLVKNTFTESAGAR.V 2 3.153 0.179

15 11 1.81

GP:AK057799_1 Homo sapiens cDNA FLJ25070 fis, 1 K.KRSDDPVEDDKEKKELGYLTVENGI 2 3.513 0.164 clone CBL05164; unnamed 0 2

GP:AB067477_1 Homo sapiens mRNA for 1 R.VWSAPLPRCVAECGASV.K 2 3.088 0.117 KIAA1890 protein, partial cds; 1 0

SW:ALFC_HUMAN fructose-bisphosphate aldolase c 1 K.YEGSGEDGGAAAQSLYIANHAY.- 2 3.191 0.124 (ec 4 3 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:E2K3_HUMAN eukaryotic translation initiation 1 R.AISPGLLVR.A 2 2.435 0.126 factor 2-alpha kinase 3 precursor 4 0

GP:AF221521_1 Homo sapiens hematopoietic PBX- 1 K.QKQPRWREGTKDSHDPLPSWA.E 2 3.999 0.172 interacting protein mRNA, 5 5 1.32

GP:BC002984_1 Homo sapiens, clone MGC:2652 1 G.WELKCPGAAGVLGPHTEYK.E 2 3.737 0.198 IMAGE:3535451, mRNA, complete 1 2 1.11

GP:AK058200_1 Homo sapiens cDNA FLJ25471 fis, 1 Q.INKLEARLRQAGCTDVRGVPR.K 2 3.038 0.111 clone TST09553; unnamed 1 2

SW:E2BB_HUMAN translation initiation factor eif-2b 1 K.LMELIR.H 1 2.322 1 beta subunit (eif-2b gdp-gtp 1 0

GP:AL079298_1 Homo sapiens mRNA full length 1 R.EGKQFSSADEAALK.E 2 3.773 0.105 insert cDNA clone EUROIMAGE 0 2

GP:AF199597_1 Homo sapiens A-type potassium 1 S.VKFEDFVTALSILLRGTVHEKLR.W 2 3.533 0.111 channel modulatory protein 1 2 0

GP:AY050169_1 Homo sapiens serum inhibited- 1 L.PMLAAYLDALQTLK.G 2 3.025 0.171 related protein (SI1) mRNA, 2 4 73.9 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF034802_1 Homo sapiens liprin-beta1 mRNA, 1 R.ALHLVEDLR.G 1 2.039 0.135 complete cds; coiled-coil protein; 1 0

GP:AL391604_3 S.pombe chromosome II cosmid 1 E.VLKNPFGLEDALTEMEK.V 2 3.026 0.148 c543; SPBC543.03c, len:696, 2 0

GP:AF074715_1 Homo sapiens mitogen- and 1 L.GTGAYGKVFLVRKAGGHDAGKLYAM 2 3.804 0.219 stress-activated protein kinase-2 4 0

PIR2:C36346 fibulin 1 precursor, splice form C - 1 R.ITYYHLSFPTNIQAPAVVFR.M 1 5.545 0.526 human 2 2 1.27 YES YES

SW:O8D2_HUMAN olfactory receptor 8d2 (olfactory 1 P.MLNPLIYSLRNKDVKNALK.K 2 3.735 0.163 receptor-like protein jcg2) 2 4 0.71 YES

SW:P2Y7_HUMAN p2y purinoceptor 7 (p2y7) 1 A.LAFLSSSVNPVLYACAGGGLLR.S 2 3.083 0.132 (leukotriene b4 receptor) 1 0

GP:AK027823_1 Homo sapiens cDNA FLJ14917 fis, 1 R.SGWVSIMAEAMK.S 1 2.432 0.148 clone PLACE1007112; unnamed 2 2 11.6

GP:BC017734_1 Homo sapiens, clone MGC:21568 1 L.NRVNLEESSGVENSPAGARPKR.K 2 3.347 0.111 IMAGE:4420306, mRNA, complete 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:A1AB_HUMAN alpha-1b adrenergic receptor 1 F.WLGYFNSCLNPIIYPCSSK.E 2 3.151 0.101 (alpha 1b-adrenoceptor) 2 0

GP:AK057806_1 Homo sapiens cDNA FLJ25077 fis, 1 H.TLNGEILRNAESGAIDVK.F 2 3.293 0.303 clone CBL06922; unnamed 2 2 1.59

SW:PLTP_HUMAN phospholipid transfer protein 1 R.MHAAFGGTFK.K 1 2.698 0.411 precursor (lipid transfer protein ii) 0 2 YES

GP:BC002863_1 Homo sapiens, clone MGC:10305 1 R.IQQAFPMHREIAVDFGLESRRD.Q 2 3.102 0.136 IMAGE:3944148, mRNA, complete 3 0

GP:BC008368_1 Homo sapiens, hypothetical 1 K.WCTPRTNNIELHYCT.G 2 3.446 0.222 protein FLJ10637, clone MGC:946 17 14 1.39

GP:AK023284_1 Homo sapiens cDNA FLJ13222 fis, 1 R.RCFQCQTKLELVQ.Q 2 3.037 0.118 clone NT2RP4002083; unnamed 0 4

SW:TPM4_HUMAN tropomyosin, fibroblast non- 1 K.EENVGLHQTLDQTLNELNCI.- 2 5.384 0.329 muscle type (tropomyosin 4) 2 0

GP:BC007827_1 Homo sapiens, Similar to RIKEN 1 G.KIRQRIMPVRNFSKFSDCTR.A 2 3.013 0.127 cDNA 1500031L02 gene, clone 2 0 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC007543_1 Homo sapiens, clone 1 D.YSRAQLLEELRR.L 2 3.057 0.181 IMAGE:2959415, mRNA, partial 2 1

GP:BC005951_1 Homo sapiens, clone MGC:14588 1 K.KGDTFSCMVGHEALPLAFTQE.T 2 4.816 0.441 IMAGE:4249174, mRNA, complete 5 2 0.9

SW:MLC1_HUMAN membrane protein mlc1 1 M.DYLRCAAGSCIPSAIVSFTVSR.R 2 3.102 0.16

0 2

GP:AJ001306_1 Homo sapiens mRNA for PDZ 1 K.ERIDTLKNDNIQALEKLEKVPD.S 2 3.084 0.128 domain protein. 1 0

SW:1AXX_HUMAN hla class i histocompatibility 1 R.WEPSSQPTIPIVGIIAGLVLLGAVIT.G 2 3.769 0.169 antigen, a-10 alpha chain 8 3 1.73

GP:AF276423_1 Homo sapiens densin-180-like 1 P.PEIGSWKNITVLFLHSNK.L 2 3.399 0.175 protein mRNA, complete cds; 2 0

SW:TF1B_HUMAN transcription intermediary factor 1- 1 K.QFNKLTEDKADVQSIIGLQRF.F 2 3.322 0.19 beta (tif1-beta) (nuclear 0 4

GP:AY057835_1 Trichechus manatus von 1 K.VIVIPVGIGPHANIK.Q 1 2.882 0.241 Willebrand factor (vWF) gene, 0 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:T23O_HUMAN tryptophan 2,3-dioxygenase (ec 1 1 R.DERNMLKVVSR.M 1 2.267 0.181

0 2

GP:AF305883_1 Gallus gallus histone 1 G.RRLFYVHYIDFNK.R 2 3.108 0.166 acetyltransferase MYST mRNA, 10 12 2.19

SW:AF6_HUMAN af-6 protein 1 K.EGVIQNFKRTLSKKEK.K 1 2.808 0.108

2 0 YES

GP:AF304164_1 Homo sapiens keratin 1 (KRT1) 1 R.THNLEPYFESFINNLR.R 2 4.248 0.444 gene, complete cds. 0 3 YES

SW:I12R_HUMAN interleukin-12 receptor beta-1 1 K.SPEVTLQLYNSVKY.E 2 3.192 0.129 chain precursor (il-12r-beta1) 5 4 1.78

SW:FRIL_HUMAN ferritin light chain (ferritin l subunit) 1 R.EGYERLLKMQNQRGGR.A 1 2.214 0.153

0 1

GP:AF363956_1 Homo sapiens hemoglobin alpha 2 1 K.TYFPHFDLSHGSAQVKGHDK.K 2 3.234 0.275 (HBA2) gene, exons 1 and 2 and 2 2 0.45

SW:XPG_HUMAN dna-repair protein complementing 1 K.EFELLDKAKGK.T 1 2.705 0.133 xp-g cells (xeroderma 2 0 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:BMP3_HUMAN bone morphogenetic protein 3 1 R.KPYKTLQAQAPEKSKNKK.K 2 3.149 0.11 precursor (bmp-3) (osteogenin) 2 0

GP:V00500_1 Human messenger RNA for beta- 1 K.SAVTAXWGK.V 1 2.687 0.303 globin; reading frame (beta- 2 0 0.56 0.21

PIR1:FGHUGB fibrinogen gamma-B chain 1 R.KMLEEIMK.Y 1 2.131 0.152 precursor [validated] - human 1 0

SW:UBPN_HUMAN ubiquitin carboxyl-terminal 1 L.FTKEEELESENAPVCDR.C 2 3.159 0.113 hydrolase 23 (ec 3.1.2.15) 1 1

PIR1:YLHUA serum amyloid A2 protein 1 R.LTGHGAEDSLADQAANK.W 1 5.511 0.507 precursor [validated] - human 2 8 4.33 YES

PIR2:I39456 serum amyloid A2-beta - human 1 R.GPGGAWAAEVISNAR.E 1 5.216 0.529

0 8 4.36

GP:BC000522_1 Homo sapiens, Similar to serine 1 R.SSTSPTTNVLLSPLSVATALSALSLG 2 5.546 0.528 (or cysteine) proteinase inhibitor, 8 8 1.02 YES

GP:S64696_1 paraoxonase B-type/arylesterase 1 K.LLPNLNDIVAVGPEHFYGTNDHYFLD 2 4.250 0.387 B-type [human, blood, liver, 4 4 1.54 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:TYSY_HUMAN thymidylate synthase (ec 2 1 F.PKLRILRKVEKIDDFK.A 2 3.261 0.136

0 2

GPN:AY013707_1 Homo sapiens ALC (ALC) mRNA, 1 G.YVPNLRNSPLEIMSR.N 2 3.315 0.201 complete cds. 0 2

SW:MPK7_HUMAN dual specificity mitogen-activated 1 K.LQEIMKQTGYLTIGGQRYQA.E 2 3.271 0.223 protein kinase kinase 7 (ec 2 1 0

SW:MLRN_HUMAN myosin regulatory light chain 2, 1 R.DGFIDKEDLHDMLASLGK.N 2 3.775 0.328 smooth muscle isoform (myosin 2 0

SW:MY7A_HUMAN myosin viia 1 A.KLAFLKLIFK.W 1 2.417 0.22

11 6 0.53

SW:LYAG_HUMAN lysosomal alpha-glucosidase 1 R.WTQLGAFYPFMR.N 1 2.668 0.138 precursor (ec 3 2 0

GP:AL132773_2 Human DNA sequence from clone 1 K.IQVQTEQ.- 1 2.29 0.067 RP4-741H3 on chromosome 20. 2 2 1.25 YES

GP:BC007319_1 Homo sapiens, SNARE protein, 1 E.YPSRVAFTLLEKVLDEFSK.Q 2 3.089 0.194 clone MGC:1281 IMAGE:2989381, 36 18 1.06 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:Y19188_1 Homo sapiens mRNA for partial 1 K.QPPEADSLSK.P 1 2.026 0.122 aczonin (acz gene). 0 1

SW:RS7_HUMAN P23821 homo sapiens (human), 1 K.VETFSGVYKKLTGKDVNFEFPE.F 2 3.237 0.173 mus musculus (mouse), and rattus 5 6 0.77

GP:AL031723_1 Human DNA sequence from clone 1 P.PGAEHKPGTHGLSGARAEMR.A 2 3.015 0.165 LA16c-439A6 on chromosome 16. 2 2 1.82

GP:AF169548_1 Homo sapiens gamma-synergin 1 K.ISKFDFLVATSQSKMKSSEE.M 2 3.102 0.131 mRNA, complete cds; contains 1 4 2 0.92

PIR2:A44265 trithorax homolog HTX, version 2 - 1 K.MENESQSKNALKESVLLPFANRVNIS 2 3.241 0.106 human 2 0

PIR2:I38170 gene hr44 protein - human 1 K.QNKALTAVGASIMTGLLGILAFAKKKK 2 3.144 0.151 (fragment) 6 7 0.88

SW:G3P1_HUMAN glyceraldehyde 3-phosphate 1 K.AGAHLKGGAK.R 1 2.82 0.376 dehydrogenase, muscle (ec 1 2 2 0.95

SW:PLSL_HUMAN l-plastin (lymphocyte cytosolic 1 K.ISTSLPVLDLIDAIQPGSINYDLLK.T 2 3.673 0.374 protein 1) (lcp-1) (lc64p) 2 4 0.8 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AJ318887_1 Homo sapiens mRNA for ASPP1 1 A.RLGDREGYVPKNLLGLYPR.I 2 3.179 0.203 protein. 6 8 0.9

PIR2:S78549 notch3 protein - human 1 R.REPVGQDALGMKNMAKGESLMGEV 2 3.757 0.122

1 0

SW:RADI_HUMAN radixin 1 K.KFVIKPIDKK.A 1 2.416 0.107

2 0

SW:RHG4_HUMAN rho-gtpase-activating protein 4 1 R.KSSLKK.G 1 2.106 1 (rho-gap hematopoietic protein 1 1

GP:Z82215_2 Human DNA sequence from clone 1 R.LKSELEDNIR.R 1 3.144 0.243 RP1-68O2 on chromosome 22 3 2 1.75

SW:SFR5_HUMAN splicing factor, arginine/serine- 1 R.SRSRSRSRTRSSSR.S 1 2.054 0.137 rich 5 (pre-mrna splicing factor 2 0

SW:TISD_HUMAN butyrate response factor 2 (tis11d 1 S.CGSAAAGGPDLYGTLK.E 2 3.800 0.182 protein) (egf-response factor 2) 3 1 1.45

SW:APM1_HUMAN adiponectin precursor (30 kda 1 K.IFYNQQNHYDGSTGK.F 2 4.308 0.495 adipocyte complement-related 0 2 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AF241830_1 Homo sapiens golgi-associated 1 K.VDSLQK.E 1 2.184 1 microtubule-binding protein 0 3

GP:AB051468_1 Homo sapiens mRNA for 1 R.IFEDHENLVENLL.N 2 3.115 0.106 KIAA1681 protein, partial cds; 1 2 4.23

SW:S108_HUMAN calgranulin a (migration inhibitory 1 K.GNFHAVYR.D 1 2.196 0.208 factor-related protein 8) (mrp-8) 0 2 YES

SW:LCAT_HUMAN phosphatidylcholine-sterol 1 R.DLLAGLPAPGVEVYCLYGVGLPTPR.T 2 3.854 0.437 acyltransferase precursor (ec 2 1 0 YES YES

SW:SRE2_HUMAN sterol regulatory element binding 1 K.LGFLASYFLSRAQSLCGPEHSAVP.D 2 3.159 0.127 protein-2 (srebp-2) (sterol 5 0

GP:AF017987_1 Homo sapiens secreted apoptosis 1 K.KIVPKKKK.P 1 2.009 0.104 related protein 2 (SARP2) mRNA, 1 1

GP:U51336_1 Human inositol 1,3,4- 1 K.NFSAGTSDR.E 1 2.374 0.116 trisphosphate 5/6-kinase mRNA, 0 2

SW:VINC_HUMAN vinculin (metavinculin) 1 K.AIPDLTAPVAAVQAAVSNLVR.- 2 4.562 0.574

4 2 0.9 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:AB033020_1 Homo sapiens mRNA for 1 V.SLQEVETEQYYSFFLVELK.E 2 3.122 0.131 KIAA1194 protein, partial cds; 1 0 YES

SW:LOL3_HUMAN lysyl oxidase homolog 3 precursor 1 K.CNCKYDGHRIWVHNCHIGDAFSEE. 2 3.149 0.188 (ec 1 0 1

GP:AB037722_1 Homo sapiens mRNA for 1 R.KLETKGYGQGPGKLK.L 1 2.906 0.201 KIAA1301 protein, partial cds; 2 8 2.67

SW:TENA_HUMAN tenascin precursor (tn) 1 V.EAARNLTVPGSLRAVDIPGLK.A 2 3.542 0.149 (hexabrachion) (cytotactin) 1 0

SW:VIL1_HUMAN villin 1 1 L.WCGKGCSGDER.E 2 3.106 0.134

0 1

SW:COF1_HUMAN cofilin, non-muscle isoform 1 K.EILVGDVGQTVDDPYATFVK.M 2 5.991 0.5

2 2 0.63

SW:DDX6_HUMAN probable atp-dependent rna 1 V.DHVQMIVLDEADK.L 2 3.257 0.121 helicase p54 (oncogene rck) 0 2

GP:AB036706_1 Homo sapiens Itln mRNA for 1 R.TDTGFLQTLGHNLFGIYQK.Y 2 3.849 0.455 intelectin, complete cds. 0 2 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:SOX4_HUMAN transcription factor sox-4 1 K.VKSGNANSSSSAAASSK.P 2 3.138 0.184

3 1 1.2

GP:AB032593_1 Homo sapiens mRNA for PXR2b, 1 V.MKEIPREESAEEK.P 2 3.040 0.109 complete cds. 0 4

SW:CAFB_HUMAN chromatin assembly factor 1 1 K.GPDGKAIVEFLSNLAR.H 1 2.663 0.186 subunit b (caf-1 subunit b) 3 0

GP:BC009890_1 Homo sapiens, hypothetical 1 R.AAAGYAACLLPGAGAR.P 1 2.347 0.102 protein FLJ11230, clone 1 0

GP:AF161449_1 Homo sapiens HSPC331 mRNA, 1 K.KEKKNRTFLRPPK.V 1 3.564 0.148 partial cds. 2 6 1.64

GP:BC012499_1 Homo sapiens, clone MGC:21066 1 A.MKYDKDEVDLLIVIGSSLKVR.P 2 3.242 0.154 IMAGE:4518906, mRNA, complete 0 4 YES

GP:BC012922_1 Homo sapiens, clone 1 S.KLCHLFLEALKENFK.V 2 3.924 0.265 IMAGE:4449401, mRNA, partial 0 1

GP:BC013767_1 Homo sapiens, Similar to RIKEN 1 R.LLLLDLSHNSLLALEPGILDTANVEAL 2 3.880 0.366 cDNA 2610528G05 gene, clone 0 2 YES Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

GP:BC017697_1 Homo sapiens, solute carrier 1 K.KQEQLKLKQLQKE.E 2 3.772 0.144 family 26, member 6, clone 0 2

GP:BC014602_1 Homo sapiens, Similar to DNA 1 K.QLEEGLK.D 1 2.708 0.156 segment, Chr 6, Miriam Meisler 5, 1 4 1

SW:PCL1_HUMAN prenylcysteine lyase precursor 1 K.KPWLAYPHYKPPEK.C 2 3.272 0.373 (ec 4 0 2

PIR2:T00415 hypothetical protein H_248O15.1 - 1 R.MLLEAENDK.E 1 2.129 0.115 human (fragment) 0 1

SW:C259_HUMAN protein c21orf59 1 V.CVTMEMVKDALDQLR.G 2 3.106 0.115

2 1 0.44

GP:AB019602_1 Homo sapiens IDN3-B mRNA, 1 S.LLTNKPALLRSLFTVGALCR.H 2 3.298 0.204 complete cds. 10 6 2.67

SW:CA1F_HUMAN collagen alpha 1(xvi) chain 1 S.GPKGGKGERGLPGPPGSKGEKGA 2 3.073 0.115 precursor 0 1

SW:MCM5_HUMAN dna replication licensing factor 1 Q.AGRPKCPLDPYFIMPDKCK.C 2 3.009 0.153 mcm5 (cdc46 homolog) (p1- 0 1 Reference Description # of different Representitive peptide Charge_state Xcorr DelCn peptides Peptide Hits Peptide Protein Standard ID overlapped with ID overlapped with reference (untreated) hits abundance ratio deviation reference [16]-- Shen et al. [27]-- Anderson et al.

SW:COMP_HUMAN cartilage oligomeric matrix protein 1 R.DGIGDACDPDADGDGVPNEK.D 2 3.668 0.296 precursor (comp) 1 0 YES

SW:MCM2_HUMAN dna replication licensing factor 1 A.GPFEVNMEETIYQNYQRIR.I 2 3.171 0.178 mcm2 (nuclear protein bm28) 5 11 1.14

SW:CRS3_HUMAN cysteine-rich secretory protein-3 1 A.NEDKDPAFTALLTTQTQVQR.E 2 3.864 0.246 precursor (crisp-3) (sgp28 2 0

SWN:CADN_HUMA cadherin 23 precursor 1 R.GIGYTIVSGNTNSIFALDYISGVLT.L 2 3.064 0.126 N (otocadherin) 0 1

SW:PAFA_HUMAN platelet-activating factor 1 R.IPQPLFFINSEYFQYPANIIK.M 2 3.609 0.258 acetylhydrolase precursor (ec 2 0 YES

SW:ANGI_HUMAN angiogenin precursor (ec 3 1 R.YTHFLTQHYDAKPQGR.D 2 4.389 0.456

2 2 0.32 Supplemental Table 2. Potentially down-regulated plasma proteins following LPS administrationa.

Reference ID Protein name Peptide hits Peptide hits Ratio of peptide hits Abundance ratio (untreated) (treated) (untreated/treated) (untreated/treated)

SW:FA5_HUMAN coagulation factor V 14 2 7

SW:APOM_HUMAN apolipoprotein m 21 10 2.1 1.7

SW:MYH9_HUMAN non-muscle myosin heavy 13 4 3.2 1.7 chain. GP:U42594_1 Human fibronectin (FN1) 10 2 5 mRNA, splice variant SW:PLEK_HUMAN pleckstrin (platelet p47 14 7 2 3.1 protein) SW:IMB3_HUMAN importin beta-3 subunit 4 0

SW:TRAD_HUMAN tumor necrosis factor 4 0 receptor type 1 associated GP:U70136_1 Human megakaryocyte 18 6 3 6.7 stimulating factor SW:BAN7_HUMAN erythrocyte band 7 integral 5 0 membrane protein SW:DDH2_HUMAN ng,ng-dimethylarginine 4 0 dimethylaminohydrolase 2\ SW:CA44_HUMAN collagen alpha 4(iv) chain 4 0

GP:AF117754_1 thyroid hormone receptor- 4 0 associated protein complex SW:RYR2_HUMAN ryanodine receptor 2 11 3 3.7 1.9

GP:AF245517_1 Homo sapiens vacuolar 4 0 proton pump 116 kDa SW:E2K3_HUMAN eukaryotic translation 4 0 initiation factor 2-alpha GP:AF074715_1 mitogen- and stress-activated 4 0 protein kinase-2 SW:SRE2_HUMAN sterol regulatory element 5 0 binding protein-2 PIR2:I54383 chromosome segregation 13 4 3.2 2.2 protein smc1 a A protein is considered as potentially down-regulated based on the same criteria as described in Table 4.