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Proteomics. 2009 Nov;9(21):4978-84. doi: 10.1002/pmic.200900326.

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

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Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany.


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 or

[Indexed for MEDLINE]

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