PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

被引：413

作者：

Deutsch, Eric W. ^{[1
]}

Lam, Henry ^{[1
]}

Aebersold, Ruedi ^{[1
,2
,3
,4
]}

机构：

[1] Inst Syst Biol, Seattle, WA 98103 USA

[2] ETH, Inst Mol Syst Biol, CH-8093 Zurich, Switzerland

[3] Univ Zurich, Fac Sci, CH-8006 Zurich, Switzerland

[4] Ctr Syst Physiol & Metabol Dis, CH-8093 Zurich, Switzerland

来源：

EMBO REPORTS | 2008年 / 9卷 / 05期

关键词：

systems biology; targeted proteomics; selected reaction monitoring;

D O I：

10.1038/embor.2008.56

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the system being studied. For proteomics to be a key part of such studies, it must deliver accurate quantification of all the components in the system for each tested perturbation without any gaps in the data. This will require a new approach to proteomics that is based on emerging targeted quantitative mass spectrometry techniques. The PeptideAtlas Project comprises a growing, publicly accessible database of peptides identified in many tandem mass spectrometry proteomics studies and software tools that allow the building of PeptideAtlas, as well as its use by the research community. Here, we describe the PeptideAtlas Project, its contents and components, and show how together they provide a unique platform to select and validate mass spectrometry targets, thereby allowing the next revolution in proteomics.

引用

页码：429 / 434

页数：6

共 26 条

[1] Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins [J].

Anderson, L ;

Hunter, CL .

MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (04) :573-588

[2] Open source system for analyzing, validating, and storing protein identification data [J].

Craig, R ;

Cortens, JP ;

Beavis, RC .

JOURNAL OF PROTEOME RESEARCH, 2004, 3 (06) :1234-1242

[3] TANDEM: matching proteins with tandem mass spectra [J].

Craig, R ;

Beavis, RC .

BIOINFORMATICS, 2004, 20 (09) :1466-1467

[4]

Desiere F, 2006, NUCLEIC ACIDS RES, V34, pD655, DOI [10.1093/nar/gkj040, 10.1007/978-1-60761-444-9_19]

[5] Review - Mass spectrometry and protein analysis [J].

Domon, B ;

Aebersold, R .

SCIENCE, 2006, 312 (5771) :212-217

[6] AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE [J].

ENG, JK ;

MCCORMACK, AL ;

YATES, JR .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1994, 5 (11) :976-989

[7]

Falkner JA, 2007, J BIOMOL TECH, V18, P3

[8] Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS [J].

Gerber, SA ;

Rush, J ;

Stemman, O ;

Kirschner, MW ;

Gygi, SP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (12) :6940-6945

[9] Ensembl 2007 [J].

Hubbard, T. J. P. ;

Aken, B. L. ;

Beal, K. ;

Ballester, B. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cunningham, F. ;

Cutts, T. ;

Down, T. ;

Dyer, S. C. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Herrero, J. ;

Holland, R. ;

Howe, K. ;

Johnson, N. ;

Kahari, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Melsopp, C. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Prlic, A. ;

Rice, S. ;

Rios, D. ;

Schuster, M. ;

Sealy, I. ;

Severin, J. ;

Slater, G. ;

Smedley, D. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. ;

Vogel, J. ;

White, S. ;

Wood, M. ;

Cox, T. ;

Curwen, V. ;

Durbin, R. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D610-D617

[10] Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search [J].

Keller, A ;

Nesvizhskii, AI ;

Kolker, E ;

Aebersold, R .

ANALYTICAL CHEMISTRY, 2002, 74 (20) :5383-5392

← 1 2 3 →