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. Author manuscript; available in PMC: 2009 Apr 1.
Published in final edited form as: Nat Methods. 2008 Sep 21;5(10):873–875. doi: 10.1038/nmeth.1254

Table 1.

List of Human Plasma PeptideAtlas Datasets Used in This Study.

Dataset Identifier Ref MS Instrument Sample Preparation a # MS runs # MS/MS spectra # Positive SEQ IDs b
HUPO-ISB/b1-CIT_glyco_lcq 27 LCQ Classic Gly,IAM,SCX 46 148536 8206 c
HUPO-ISB/NIBSC_glyco_lcq 27 LCQ Classic Gly,IAM,SCX 47 157370 18486 c
HUPOPPP12/HUPO12_run31 27 LCQ Deca Alb,Ig,IAM,SCX 15 27007 1041 d
HUPOPPP12/HUPO12_run32 27 LCQ Deca Alb,Ig,IAM,SCX 15 29383 1292 d
HUPOPPP12/HUPO12_run33 27 LCQ Deca Alb,Ig,IAM,SCX 15 24726 1463 d
HUPOPPP12/HUPO12_run34 27 LCQ Deca Alb,Ig,IAM,SCX 15 21311 1043 d
HUPOPPP22/HUPO22_M_CA_S 27 LCQ Deca XP Top6,IAM,SCX 219 517747 11706 d
HUPOPPP28/HUPO28_b1-CIT 27 LCQ Duo None 1 3570 412 c
HUPOPPP28/HUPO28_b1-SERUM 27 LCQ Duo None 1 3640 529 c
HUPOPPP28/HUPO28_b2-CIT 27 LCQ Duo None 5 12534 2032 c
HUPOPPP28/HUPO28_b2-SERUM 27 LCQ Duo None 5 12483 1676 c
HUPOPPP28/HUPO28_b3-CIT 27 LCQ Duo None 1 3631 578 c
HUPOPPP28/HUPO28_b3-SERUM 27 LCQ Duo None 1 3618 583 c
HUPOPPP28/HUPO28_Ref-CIT 27 LCQ Duo None 1 3543 413 c
HUPOPPP28/HUPO28_Ref-SERUM 27 LCQ Duo None 1 3546 366 c
HUPOPPP29/HUPO29_b1-CIT_1 27 LCQ Deca XP Top6,IAM,SCX 17 132484 6313 c
HUPOPPP29/HUPO29_b1-CIT_win1 27 LCQ Deca XP Top6,IAM,SCX 15 106995 3205 c
HUPOPPP29/HUPO29_b1-CIT_win2 27 LCQ Deca XP Top6,IAM,SCX 15 90803 657 c
HUPOPPP29/HUPO29_b1-EDTA_1 27 LCQ Deca XP Top6,IAM,SCX 15 130894 1250 c
HUPOPPP29/HUPO29_b1-EDTA_win1 27 LCQ Deca XP Top6,IAM,SCX 15 112090 6117 c
HUPOPPP29/HUPO29_b1-EDTA_win2 27 LCQ Deca XP Top6,IAM,SCX 14 84068 2286 c
HUPOPPP29/HUPO29_b1-HEP 27 LCQ Deca XP Top6,IAM,SCX 15 133616 762 c
HUPOPPP29/HUPO29_b1-SERUM 27 LCQ Deca XP Top6,IAM,SCX 15 129002 2057 c
HUPOPPP34/HUPO34 27 LCQ Deca XP Top6,IAM,pI,Size 140 477321 13522 c
HUPOPPP34/HUPO34_b1-SERUM 27 LTQ Top6,IAM,pI,Size 157 1116626 75221 d
HUPOPPP37/HUPO37_b1-HEP_2LCQ 27 LCQ Deca XP None 17 10953 27 c
HUPOPPP40/HUPO40 27 LCQ Alb,Ig,IAM,SCX 126 66695 6124 c
wqian/HsPlasma_tryp_nonalkylated 28 LCQ Deca XP Alb,Ig,SCX 321 451115 141852 e
wqian/HsPlasma_tryp_alkylated 28 LCQ Duo Alb,Ig,SCX,IAM 140 2277496 46480 e
mpeitsch/NovartisPlasma/MicroProt 29 Bruker Esquire Alb,Ig,IAM,Size,SCX 38252 5741424 284100 c
mpeitsch/NovartisPlasma/MicroProt2 29 Bruker Esquire Alb,Ig,IAM,Size,SCX 7480 2522032 480193 d
apaulovich/serum_fractionation/01_glyco 30 LTQ Gly,IAM 10 171207 33789 c
apaulovich/serum_fractionation/15_clinprot_c3 30 LTQ HIC,IAM 10 138430 14891 c
apaulovich/serum_fractionation/16_clinprot_c8 30 LTQ HIC,IAM 10 142338 13999 c
apaulovich/serum_fractionation/17_wcx 30 LTQ WCX,IAM 10 147259 26813 c
apaulovich/serum_fractionation/18_size 30 LTQ Size,IAM 10 166796 19813 c
apaulovich/serum_fractionation/19_proteintag 30 LTQ Ig,IAM 10 155402 8556 c
apaulovich/serum_fractionation/20_cys 30 LTQ Cys,IAM 10 150152 31852 c
apaulovich/serum_fractionation/21_unfract 30 LTQ IAM 10 74936 16013 c
apaulovich/serum_fractionation/22_mars 30 LTQ Top6,IAM 10 194523 37004 c
a

Abbreviations for sample preparation: Alb = albumin depletion, Ig = Immunoglobulin depletion, Top6 = Depletion of 6 highest-abundance serum proteins, Gly: glycocapture enrichment, Cys: cysteinyl chemistry enrichment, IAM: alkylation of cysteines by iodoacetamide, SCX: strong cation exchange, pI: fractionation based on isoelectric point, Size: fractionation based on size, HIC: hydrophobic interaction chromatography, WCX: weak cation exchange.

b

SEQUEST identifications with PeptideProphet-estimated probabilities at or above 0.9.

c

Searched against human IPI (International Protein Index) database version 3.21;

d

Searched against human IPI database version 3.17;

e

Searched against human IPI database version 3.16.