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

被引：60

作者：

Renard, Bernhard Y. ^{[2
]}

Kirchner, Marc ^{[2
,3
]}

Monigatti, Flavio ^{[3
]}

Ivanov, Alexander R. ^{[4
]}

Rappsilber, Juri ^{[5
]}

Winter, Dominic ^{[3
]}

Steen, Judith A. J. ^{[6
,7
]}

Hamprecht, Fred A. ^{[2
]}

Steen, Hanno ^{[1
,3
]}

机构：

[1] Childrens Hosp, Dept Pathol, Prote Ctr, Boston, MA 02115 USA

[2] Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Heidelberg, Germany

[3] Harvard Univ, Sch Med, Dept Pathol, Boston, MA 02115 USA

[4] Harvard Univ, Sch Publ Hlth, Dept Genet & Complex Dis, Boston, MA 02115 USA

[5] Univ Edinburgh, Wellcome Trust Ctr Cell Biol, Edinburgh, Midlothian, Scotland

[6] Harvard Univ, Sch Med, Dept Neurobiol, Boston, MA 02115 USA

[7] Childrens Hosp, Dept Neurol, Boston, MA 02115 USA

来源：

PROTEOMICS | 2009年 / 9卷 / 21期

关键词：

TANDEM MASS-SPECTRA; PROTEIN IDENTIFICATION; SPECTROMETRY DATA; QUALITY ASSESSMENT; ALGORITHMS; PROTEOMICS; DATABASE; MASCOT; RATES;

D O I：

10.1002/pmic.200900326

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：4978 / 4984

页数：7

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