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

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 preprocessin...

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Bibliographic Details
Published in:Proteomics (Weinheim) 2009-11, Vol.9 (21), p.4978-4984
Main Authors: Renard, Bernhard Y, Kirchner, Marc, Monigatti, Flavio, Ivanov, Alexander R, Rappsilber, Juri, Winter, Dominic, Steen, Judith A.J, Hamprecht, Fred A, Steen, Hanno
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Animals
Biological and medical sciences
Computational Biology - methods
Fundamental and applied biological sciences. Psychology
Humans
Internet
Miscellaneous
Peptides - analysis
Peptides - chemistry
Proteins
Proteomics - methods
Software Design
Tandem Mass Spectrometry - methods
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Summary: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.
ISSN:1615-9853
1615-9861
1615-9861
DOI:10.1002/pmic.200900326