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 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.
Renard
Bernhard Y
BY
Interdisciplinary Center for Scientific Computing, University of Heidelberg, Heidelberg, Germany.
Kirchner
Marc
M
Monigatti
Flavio
F
Ivanov
Alexander R
AR
Rappsilber
Juri
J
Winter
Dominic
D
Steen
Judith A J
JA
Hamprecht
Fred A
FA
Steen
Hanno
H
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*
D010455:Peptides