A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time.

BMC Bioinformatics
Hua XuMichael A Freitas

Abstract

Rejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine and improve peptide identifications from database search algorithms. This report describes the implementation of an automated approach to reduce false positives and validate peptide matches. A robust linear regression based algorithm was developed to automate the evaluation of peptide identifications obtained from shotgun proteomic experiments. The algorithm scores peptides based on their predicted and observed reversed-phase liquid chromatography retention times. The robust algorithm does not require internal or external peptide standards to train or calibrate the linear regression model used for peptide retention time prediction. The algorithm is generic and can be incorporated into any database search program to perform automated evaluation of the candidate peptide matches based on their retention times. It provides a statistical score for each peptide match based on its retention time. Analysis of peptide matches where the retention time score was included resulted in a significant reduction of false positive matches wi...Continue Reading

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Citations

Jan 31, 2012·Journal of the American Chemical Society·Jason L SeitchikRyan A Mehl
Mar 12, 2011·Chemical Research in Toxicology·Chenqi HuRichard B van Breemen
Mar 24, 2009·Bioinformatics·Hua Xu, Michael A Freitas
Jun 21, 2011·BMC Bioinformatics·Marcin J MiziantyLukasz Kurgan
Apr 25, 2014·European Journal of Pharmaceutics and Biopharmaceutics : Official Journal of Arbeitsgemeinschaft Für Pharmazeutische Verfahrenstechnik E.V·Amber Haynes FradkinTheodore W Randolph
May 23, 2014·Journal of the American Society for Mass Spectrometry·Michelle R RobinsonJennifer S Brodbelt
Oct 26, 2011·Journal of Molecular Biology·Yun-Jeong KimDavid M Wilson
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Feb 18, 2014·Biochemical and Biophysical Research Communications·Zhengyi ChenGuihua Ruan
Oct 15, 2013·Molecular Cell·Christophe RouillonMalcolm F White
Jun 5, 2016·Journal of Proteomics·Owen E Branson, Michael A Freitas
Mar 20, 2019·Frontiers in Genetics·Shuai LiuYongchun Zuo
Jan 24, 2021·Journal of Chromatography. a·Alexander KensertDeirdre Cabooter
Jun 21, 2021·Molecular Reproduction and Development·Emily E KillingbeckWillie J Swanson

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Software Mentioned

MassMatrix
SEQUEST
mzData
RT
Tandem
Perl scripts
LR
! Tandem
Global Proteome Machine
Mascot

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