Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Brusniak, Mi Youn ^a   Bodenmiller, Bernd ^b   Campbell, David ^a   Cooke, Kelly ^a   Eddes, James ^a   Garbutt, Andrew ^a   Lau, Hollis ^a   Letarte, Simon ^a   Mueller, Lukas N ^b   Sharma, Vagisha ^a   Vitek, Olga ^c   Zhang, Ning ^a   Aebersold, Ruedi ^a,b,c,d   Watts, Julian D ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b ETH ZURICH   (Switzerland)

^c Purdue University   (United States)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL FRAMEWORK; COMPUTATIONAL PLATFORMS; LIQUID CHROMATOGRAPHY - MASS SPECTROMETRIES; MICROARRAY DATA ANALYSIS; QUANTITATIVE PROTEOMICS; SEQUENCE IDENTIFICATION; STATISTICAL DATA ANALYSIS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; BIOINFORMATICS; DATA PROCESSING; DISTRIBUTED COMPUTER SYSTEMS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR BIOLOGY; PEPTIDES; RESEARCH; SOFTWARE ENGINEERING; STATISTICAL METHODS; TOOLS; USER INTERFACES;

PROCESS CONTROL;

PROTEIN; PROTEOME;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; INTERNET; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHODOLOGY; PROTEOMICS;

CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; INTERNET; MASS SPECTROMETRY; PROTEINS; PROTEOME; PROTEOMICS; SOFTWARE;

EID: 62149110095     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-542     Document Type: Article

References (32)

1. Aebersold R Mann M Mass spectrometry-based proteomics Nature 2003, 422(6928):198-207. 10.1038/nature01511 12634793
2. Gillette MA Mani DR Carr SA Place of pattern in proteomic biomarker discovery J Proteome Res 2005, 4(4):1143-1154. 10.1021/pr0500962 16083265
3. MacCoss MJ Matthews DE Quantitative MS for proteomics: Teaching a new dog old tricks Anal Chem 2005, 77(15):294A-302A. 10.1021/ac053431e 16134292
4. Mueller LN Brusniak MY Mani DR Aebersold R An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data J Proteome Res 2008, 7(1):51-61. 10.1021/pr700758r 18173218
5. Gygi SP Rist B Gerber SA Turecek F Gelb MH Aebersold R Quantitative analysis of complex protein mixtures using isotope-coded affinity tags Nat Biotechnol 1999, 17(10):994-999. 10.1038/13690 10504701
6. Ross PL Huang YN Marchese JN Williamson B Parker K Hattan S Khainovski N Pillai S Dey S Daniels S Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol Cell Proteomics 2004, 3(12):1154-1169. 10.1074/mcp.M400129-MCP200 15385600
7. Ong SE Blagoev B Kratchmarova I Kristensen DB Steen H Pandey A Mann M Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol Cell Proteomics 2002, 1(5):376-386. 10.1074/mcp.M200025-MCP200 12118079
8. Bellew M Coram M Fitzgibbon M Igra M Randolph T Wang P May D Eng J Fang R Lin C A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS Bioinformatics 2006, 22(15):1902-1909. 10.1093/bioinformatics/btl276 16766559
9. Du P Sudha R Prystowsky MB Angeletti RH Data reduction of isotope-resolved LC-MS spectra Bioinformatics 2007, 23(11):1394-1400. 10.1093/bioinformatics/btm083 17496000
10. Jaffe JD Mani DR Leptos KC Church GM Gillette MA Carr SA PEPPeR, a platform for experimental proteomic pattern recognition Mol Cell Proteomics 2006, 5(10):1927-1941. 10.1074/mcp.M600222-MCP200 16857664
11. Katajamaa M Miettinen J Oresic M MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data Bioinformatics 2006, 22(5):634-636. 10.1093/bioinformatics/btk039 16403790
12. Li XJ Yi EC Kemp CJ Zhang H Aebersold R A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry Mol Cell Proteomics 2005, 4(9):1328-1340. 10.1074/mcp.M500141-MCP200 16048906
13. May D Fitzgibbon M Liu Y Holzman T Eng J Kemp CJ Whiteaker J Paulovich A McIntosh M A platform for accurate mass and time analyses of mass spectrometry data J Proteome Res 2007, 6(7):2685-2694. 10.1021/pr070146y 17559252
14. Mayr BM Kohlbacher O Reinert K Sturm M Gropl C Lange E Klein C Huber CG Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography-electrospray ionization mass spectrometry and novel data analysis algorithms J Proteome Res 2006, 5(2):414-421. 10.1021/pr050344u 16457608
15. Mueller LN Rinner O Schmidt A Letarte S Bodenmiller B Brusniak MY Vitek O Aebersold R Muller M SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling Proteomics 2007, 7(19):3470-3480. 10.1002/pmic.200700057 17726677
16. Smith CA Want EJ O'Maille G Abagyan R Siuzdak G XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal Chem 2006, 78(3):779-787. 10.1021/ac051437y 16448051
17. Seattle Proteome Center (SPC) - Corra http://tools.proteomecenter.org/ Corra/corra.html
18. Desiere F Deutsch EW Nesvizhskii AI Mallick P King NL Eng JK Aderem A Boyle R Brunner E Donohoe S Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry Genome Biol 2005, 6(1):R9. 549070 15642101 10.1186/gb-2004-6-1-r9
19. Zhang H Loriaux P Eng J Campbell D Keller A Moss P Bonneau R Zhang N Zhou Y Wollscheid B UniPep-a database for human N-linked glycosites: A resource for biomarker discovery Genome Biol 2006, 7(8):R73. 1779586 16901351 10.1186/gb-2006-7-8-r73
20. Bioconductor: Open source software for bioinformatics http:// www.bioconductor.org/
21. Smyth GK Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 2004, 3. 16646809
22. Conesa A Nueda MJ Ferrer A Talon M maSigPro: A method to identify significantly differential expression profiles in time-course microarray experiments Bioinformatics 2006, 22(9):1096-1102. 10.1093/bioinformatics/ btl056 16481333
23. Keller A Eng J Zhang N Li XJ Aebersold R A uniform proteomics MS/MS analysis platform utilizing open XML file formats Mol Syst Biol 2005, 1. 1681455 16729052
24. Proteomic and metabolomic approaches to diagnose diabetes and pre-diabetes http://grants.nih.gov/grants/guide/pa-files/PAR-04-076.html
25. Zhou Y Aebersold R Zhang H Isolation of N-linked glycopeptides from plasma Anal Chem 2007, 79(15):5826-5837. 10.1021/ac0623181 17591751
26. Schmidt A Gehlenborg N Bodenmiller B Mueller LN Campbell D Mueller M Aebersold R Domon B An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures Mol Cell Proteomics 2008, 7(11):2138-2150. 10.1074/mcp.M700498-MCP200 18511481
27. Bodenmiller B Mueller LN Mueller M Domon B Aebersold R Reproducible isolation of distinct, overlapping segments of the phosphoproteome Nat Methods 2007, 4(3):231-237. 10.1038/nmeth1005 17293869
28. Bodenmiller B Mueller LN Pedrioli PG Pflieger D Junger MA Eng JK Aebersold R Tao WA An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: Application to Drosophila melanogaster Kc167 cells Mol Biosyst 2007, 3(4):275-286. 10.1039/b617545g 17372656
29. Keller A Nesvizhskii AI Kolker E Aebersold R Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal Chem 2002, 74(20):5383-5392. 10.1021/ac025747h 12403597
30. Pedrioli PG Eng JK Hubley R Vogelzang M Deutsch EW Raught B Pratt B Nilsson E Angeletti RH Apweiler R A common open representation of mass spectrometry data and its application to proteomics research Nat Biotechnol 2004, 22(11):1459-1466. 10.1038/nbt1031 15529173
31. Gentleman R Carey V Huber W Irizarry R Dudoit S Bioinformatics and Computational Biology Solutions Using R and Bioconductor New York: Springer 2005.
32. Ko GT Chan JC Woo J Lau E Yeung VT Chow CC Cockram CS The reproducibility and usefulness of the oral glucose tolerance test in screening for diabetes and other cardiovascular risk factors Ann Clin Biochem 1998, 35(Pt 1):62-67. 9463740