When less can yield more – Computational preprocessing of MS/MS spectra for peptide identification | Zendy

Renard Bernhard Y. | Zendy; Kirchner Marc | Zendy; Monigatti Flavio | Zendy; Ivanov Alexander R. | Zendy; Rappsilber Juri | Zendy; Winter Dominic | Zendy; Steen Judith A. J. | Zendy; Hamprecht Fred A. | Zendy; Steen Hanno | Zendy

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

Author(s) -

Renard Bernhard Y.,

Kirchner Marc,

Monigatti Flavio,

Ivanov Alexander R.,

Rappsilber Juri,

Winter Dominic,

Steen Judith A. J.,

Hamprecht Fred A.,

Steen Hanno

Publication year - 2009

Publication title -

proteomics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.26

H-Index - 167

eISSN - 1615-9861

pISSN - 1615-9853

DOI - 10.1002/pmic.200900326

Subject(s) - preprocessor , mascot , identification (biology) , spurious relationship , computer science , database search engine , software , mass spectrometry , proteomics , data pre processing , sensitivity (control systems) , mass spectrum , data mining , chemistry , artificial intelligence , chromatography , search engine , machine learning , biology , information retrieval , engineering , operating system , biochemistry , botany , electronic engineering , political science , gene , law

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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