When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification

Bernard Y. Renard, Marc Kirchner, Flavio Monigatti, Alexander R. Ivanov, Juri Rappsilber, Dominic Winter, Judith A.J. Steen, Fred A. Hamprecht, Hanno Steen

Research output: Contribution to journalArticlepeer-review

Abstract

The effectiveness of database search algorithms, such as Mascot, Sequest and ProteinPilot is limited by the quality of the input spectra: spurious peaks in MS/MS spectra can jeopardize the correct identification of peptides or reduce their score significantly. Consequently, an efficient preprocessing of MS/MS spectra can increase the sensitivity of peptide identification at reduced file sizes and run time without compromising its specificity. We investigate the performance of 25 MS/MS preprocessing methods on various data sets and make software for improved preprocessing of mgf/dta-files freely available from http://hci.iwr.uni-heidelberg. de/mip/proteomics or http://www. childrenshospital.org/research/steenlab.
Original languageEnglish
Pages (from-to)4978-4984
Number of pages7
JournalProteomics
Volume9
Issue number21
Early online date9 Sep 2009
DOIs
Publication statusPublished - 30 Nov 2009

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