A nonparametric model for quality control of database search results in shotgun proteomics.

BMC Bioinformatics
Jiyang ZhangFuchu He

Abstract

Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recently, methods based on a randomized database have become popular for quality control of database search results. However, a consequent problem is the ignorance of how to combine different database search scores to improve the sensitivity of randomized database methods. In this paper, a multivariate nonlinear discriminate function (DF) based on the multivariate nonparametric density estimation technique was used to filter out false-positive database search results with a predictable false positive rate (FPR). Application of this method to control datasets of different instruments (LCQ, LTQ, and LTQ/FT) yielded an estimated FPR close to the actual FPR. As expected, the method was more sensitive when more features were used. Furthermore, the new method was shown to be more sensitive than two commonly used methods on 3 complex sample datasets and 3 control datasets. Using the nonparametric model, a more flexible DF can be obtained, resulting in improved sensitivity and good FPR estimation. This nonparametric statistical technique...Continue Reading

References

Jul 15, 1999·Nature Biotechnology·A J LinkJ R Yates
Jun 24, 2000·Nature·A Pandey, M Mann
Apr 16, 2002·Journal of the American Society for Mass Spectrometry·Roger E MooreTerry D Lee
Mar 1, 2003·Nature Genetics·Scott D Patterson, Ruedi H Aebersold
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
Feb 13, 2004·Drug Discovery Today·Alexey I Nesvizhskii, Ruedi Aebersold
Mar 17, 2004·Analytical Chemistry·Tomasz BaczekRoman Kaliszan
Apr 17, 2004·Nature Biotechnology·John T PrinceEdward M Marcotte
Apr 27, 2004·Omics : a Journal of Integrative Biology·Samuel PurvineEugene Kolker
Jul 2, 2004·Analytical Chemistry·Katheryn A ResingNatalie G Ahn
Jul 30, 2004·Rapid Communications in Mass Spectrometry : RCM·Fuxin LiJue Wang
Oct 12, 2004·Journal of Proteome Research·Xiaoyu YangJeffrey A Kowalak
Oct 19, 2004·Molecular & Cellular Proteomics : MCP·Wei SunYouhe Gao
Jan 7, 2005·Nature·Jens S AndersenMatthias Mann
May 26, 2005·Bioinformatics·Julia HandlDouglas B Kell
Aug 25, 2005·Nature Methods·Daniel Chamrad, Helmut E Meyer
Dec 3, 2005·Molecular & Cellular Proteomics : MCP·Peter J UlintzPhilip C Andrews
Jan 13, 2006·Omics : a Journal of Integrative Biology·Roger HigdonEugene Kolker
Apr 15, 2006·Science·Bruno Domon, Ruedi Aebersold
Apr 26, 2006·Molecular & Cellular Proteomics : MCP·Wilhelm HaasSteven P Gygi
May 6, 2006·Journal of Proteome Research·Patrick A EverleySteven P Gygi
May 20, 2006·Genome Biology·Bartosz Pilch, Matthias Mann
Aug 10, 2006·Molecular & Cellular Proteomics : MCP·Bruno Domon, Ruedi Aebersold
Oct 5, 2006·Molecular & Cellular Proteomics : MCP·Shaojun SunKatheryn A Resing
Jul 12, 2007·Proteomics·Ming ChenXiaohong Qian
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Nov 14, 2008·Molecular & Cellular Proteomics : MCP·Jiyang ZhangFuchu He
Jul 15, 2009·Molecular & Cellular Proteomics : MCP·Vittoria MataforaAngela Bachi
Mar 1, 2012·Briefings in Bioinformatics·Ting HuangZengyou He
Nov 26, 2008·Critical Reviews in Biotechnology·Lei NieWeiwen Zhang
Jul 24, 2013·Journal of Proteome Research·Jiyang ZhangHongwei Xie

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Software Mentioned

Peptideprophet
OutSum
MASCOT
Extract
Sim
NoParQ
TurboSEQUEST
Matlab script
SEQUEST
. exe

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