VIPER: an advanced software package to support high-throughput LC-MS peptide identification

被引:162
作者
Monroe, Matthew E. [1 ]
Tolic, Nikola [1 ]
Jaitly, Navdeep [1 ]
Shaw, Jason L. [1 ]
Adkins, Joshua N. [1 ]
Smith, Richard D. [1 ]
机构
[1] Pacific NW Natl Lab, Richland, WA 99354 USA
关键词
D O I
10.1093/bioinformatics/btm281
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides previously identified in LC-MS/MS analyses, and identify and quantify pairs of isotopically labeled peptides.
引用
收藏
页码:2021 / 2023
页数:3
相关论文
共 11 条
[1]   Estimating probabilities of peptide database identifications to LC-FTICR-MS observations [J].
Anderson, Kevin K. ;
Monroe, Matthew E. ;
Daly, Don S. .
PROTEOME SCIENCE, 2006, 4 (1)
[2]   TANDEM: matching proteins with tandem mass spectra [J].
Craig, R ;
Beavis, RC .
BIOINFORMATICS, 2004, 20 (09) :1466-1467
[3]   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
[4]   Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics [J].
Hixson, Kim K. ;
Adkins, Joshua N. ;
Baker, Scott E. ;
Moore, Ronald J. ;
Chromy, Brett A. ;
Smith, Richard D. ;
McCutchen-Maloney, Sandra L. ;
Lipton, Mary S. .
JOURNAL OF PROTEOME RESEARCH, 2006, 5 (11) :3008-3017
[5]   Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules [J].
Horn, DM ;
Zubarev, RA ;
McLafferty, FW .
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2000, 11 (04) :320-332
[6]   Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline [J].
Jaitly, Navdeep ;
Monroe, Matthew E. ;
Petyuk, Vladislav A. ;
Clauss, Therese R. W. ;
Adkins, Joshua N. ;
Smith, Richard D. .
ANALYTICAL CHEMISTRY, 2006, 78 (21) :7397-7409
[7]   A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry [J].
Li, XJ ;
Pedrioli, PGA ;
Eng, J ;
Martin, D ;
Yi, EC ;
Lee, H ;
Aebersold, R .
ANALYTICAL CHEMISTRY, 2004, 76 (13) :3856-3860
[8]  
Perkins DN, 1999, ELECTROPHORESIS, V20, P3551, DOI 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO
[9]  
2-2
[10]   Large-scale analysis of the yeast proteome by multidimensional protein identification technology [J].
Washburn, MP ;
Wolters, D ;
Yates, JR .
NATURE BIOTECHNOLOGY, 2001, 19 (03) :242-247