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.
authors.affiliation: Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany.
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
authors.forename: Marc
authors.initials: M
authors.lastname: Kirchner
authors.forename: Flavio
authors.initials: F
authors.lastname: Monigatti
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Ivanov
authors.forename: Juri
authors.initials: J
authors.lastname: Rappsilber
authors.forename: Dominic
authors.initials: D
authors.lastname: Winter
authors.forename: Judith A J
authors.initials: JA
authors.lastname: Steen
authors.forename: Fred A
authors.initials: FA
authors.lastname: Hamprecht
authors.forename: Hanno
authors.initials: H
authors.lastname: Steen
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020407:Internet; D010455:Peptides / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012985:Software Design; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides