title: A large, consistent plasma proteomics data set from prospectively collected breast cancer patient and healthy volunteer samples.
abstract: BACKGROUND
  Variability of plasma sample collection and of proteomics technology platforms has been detrimental to generation of large proteomic profile datasets from human biospecimens.
  
  
  METHODS
  We carried out a clinical trial-like protocol to standardize collection of plasma from 204 healthy and 216 breast cancer patient volunteers. The breast cancer patients provided follow up samples at 3 month intervals. We generated proteomics profiles from these samples with a stable and reproducible platform for differential proteomics that employs a highly consistent nanofabricated ChipCube™ chromatography system for peptide detection and quantification with fast, single dimension mass spectrometry (LC-MS). Protein identification is achieved with subsequent LC-MS/MS analysis employing the same ChipCube™ chromatography system.
  
  
  RESULTS
  With this consistent platform, over 800 LC-MS plasma proteomic profiles from prospectively collected samples of 420 individuals were obtained. Using a web-based data analysis pipeline for LC-MS profiling data, analyses of all peptide peaks from these plasma LC-MS profiles reveals an average coefficient of variability of less than 15%. Protein identification of peptide peaks of interest has been achieved with subsequent LC-MS/MS analyses and by referring to a spectral library created from about 150 discrete LC-MS/MS runs. Verification of peptide quantity and identity is demonstrated with several Multiple Reaction Monitoring analyses. These plasma proteomic profiles are publicly available through ProteomeCommons.
  
  
  CONCLUSIONS
  From a large prospective cohort of healthy and breast cancer patient volunteers and using a nano-fabricated chromatography system, a consistent LC-MS proteomics dataset has been generated that includes more than 800 discrete human plasma profiles. This large proteomics dataset provides an important resource in support of breast cancer biomarker discovery and validation efforts.
authors: Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA.
authors: Catherine P
authors: CP
authors: Riley
authors: Xiang
authors: X
authors: Zhang
authors: Harikrishna
authors: H
authors: Nakshatri
authors: Bryan
authors: B
authors: Schneider
authors: Fred E
authors: FE
authors: Regnier
authors: Jiri
authors: J
authors: Adamec
authors: Charles
authors: C
authors: Buck
references: Clin Exp Metastasis. 2010 Aug;27(6):441-51
references: 20607365
references: Anal Chim Acta. 2010 Apr 7;664(2):101-13
references: 20363391
references: Proteomics Clin Appl. 2007 Mar;1(3):246-63
references: 21136676
references: Rapid Commun Mass Spectrom. 2006;20(21):3236-44
references: 17016832
references: J Proteome Res. 2010 Oct 1;9(10):4982-91
references: 20677825
references: J Sep Sci. 2010 Jun;33(10):1421-37
references: 20486207
references: Proteomics Clin Appl. 2010 Dec;4(12):904-14
references: 21137031
references: Proteomics. 2009 Oct;9(20):4653-63
references: 19795424
references: Anal Chem. 2005 Mar 15;77(6):1631-40
references: 15762566
references: BMC Med Genomics. 2008 Sep 15;1:41
references: 18793429
references: Electrophoresis. 1999 Dec;20(18):3551-67
references: 10612281
references: J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
references: 24226387
references: Clin Chim Acta. 2001 Oct;312(1-2):13-23
references: 11580905
references: Front Biosci (Landmark Ed). 2009 Jan 01;14:3292-303
references: 19273274
references: Anal Chem. 2010 Oct 15;82(20):8696-702
references: 20845935
references: Proteomics. 2008 Feb;8(4):731-49
references: 18297651
references: Prostate. 1997 Oct 1;33(2):87-96
references: 9316649
references: World J Gastroenterol. 1998 Aug;4(4):337-339
references: 11819315
references: Rapid Commun Mass Spectrom. 2003;17(20):2310-6
references: 14558131
references: Nat Biotechnol. 2009 Jul;27(7):633-41
references: 19561596
references: J Natl Cancer Inst. 2010 Oct 6;102(19):1462-7
references: 20705936
references: Nature. 2008 Apr 3;452(7187):571-9
references: 18385731
references: Trends Biotechnol. 2002 Dec;20(12 Suppl):S1-2
references: 12570151
references: Am J Physiol Heart Circ Physiol. 2009 Apr;296(4):H1184-92
references: 19218503
references: J Chromatogr A. 2000 Feb 18;870(1-2):295-313
references: 10722087
references: Nat Methods. 2007 Oct;4(10):787-97
references: 17901868
references: J Proteome Res. 2010 Apr 5;9(4):1902-12
references: 20078137
references: Nat Biotechnol. 1999 Oct;17(10):994-9
references: 10504701
references: Anal Biochem. 2004 Oct 1;333(1):174-81
references: 15351294
references: OMICS. 2010 Dec;14(6):689-99
references: 20958246
references: Bioinformatics. 2005 Nov 1;21(21):4054-9
references: 16150809
references: Proteomics. 2002 May;2(5):513-23
references: 11987125
references: Anal Chem. 2004 Jul 15;76(14):4193-201
references: 15253663
references: Bioinformatics. 2010 Apr 1;26(7):966-8
references: 20147306
references: J Proteome Res. 2010 Feb 5;9(2):730-6
references: 19957947
references: Proteomics. 2010 Apr;10(7):1416-25
references: 20127685
references: Anal Chem. 2005 Jan 15;77(2):527-33
references: 15649049
references: Proteomics Clin Appl. 2009 Nov;3(11):1305-13
references: 21136952
references: Anticancer Res. 2007 May-Jun;27(3A):1247-55
references: 17593616
references: Mol Cell Proteomics. 2006 Jul;5(7):1338-47
references: 16552026
references: J Proteomics Bioinform. 2009 Oct 2;2:416-438
references: 20473349
references: Nat Biotechnol. 2006 Aug;24(8):905-8
references: 16900126
references: Nature. 2006 Jun 15;441(7095):840-6
references: 16699522
references: Biomed Chromatogr. 2009 May;23(5):480-7
references: 19039805
references: Nat Methods. 2009 Jun;6(6):423-30
references: 19448641
references: Brief Funct Genomic Proteomic. 2009 Mar;8(2):145-57
references: 19279071
references: Proteomics. 2005 Aug;5(13):3475-90
references: 16047398
references: J Am Soc Mass Spectrom. 2005 Jul;16(7):1181-91
references: 15922621
references: J Sep Sci. 2006 Mar;29(4):499-509
references: 16583688
references: Anal Bioanal Chem. 2007 Oct;389(4):1017-31
references: 17668192
references: Mol Cell Proteomics. 2006 Jul;5(7):1233-44
references: 16571896
references: J Mass Spectrom. 2002 Feb;37(2):133-45
references: 11857757