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Supporting Information for Proteomics DOI 10.1002/Pmic.200400942

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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.
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