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

doi:10.1002/pmic.200900326

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

School of Biological Sciences

Research output: Contribution to journal › Article › peer-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 language	English
Pages (from-to)	4978-4984
Number of pages	7
Journal	Proteomics
Volume	9
Issue number	21
Early online date	9 Sep 2009
DOIs	https://doi.org/10.1002/pmic.200900326
Publication status	Published - 30 Nov 2009

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title = "When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification",

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.",

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AU - Renard, Bernard Y.

AU - Kirchner, Marc

AU - Monigatti, Flavio

AU - Ivanov, Alexander R.

AU - Rappsilber, Juri

AU - Winter, Dominic

AU - Steen, Judith A.J.

AU - Hamprecht, Fred A.

AU - Steen, Hanno

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AB - 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.

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

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