FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data

被引：16

作者：

Barsnes, Harald ^{[1
]}

Eidhammer, Ingvar ^{[1
]}

Martens, Lennart ^{[2
,3
]}

机构：

[1] Univ Bergen, Dept Informat, N-5020 Bergen, Norway

[2] Univ Ghent VIB, Dept Med Prot Res, Ghent, Belgium

[3] Univ Ghent, Dept Biochem, B-9000 Ghent, Belgium

来源：

PROTEOMICS | 2010年 / 10卷 / 05期

关键词：

Bioinformatics; MS fragmentation; MS/MS; Post-translational modification; INDUCED DISSOCIATION SPECTRA; OPEN-SOURCE LIBRARY; MASS-SPECTROMETRY; PREDICTION; PROTEOMICS; PEPTIDES; PARSE;

D O I：

10.1002/pmic.200900681

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A thorough understanding of the fragmentation processes in MS/MS can be a powerful tool in assessing the resulting peptide and protein identifications. We here present the freely available, open-source FragmentationAnalyzer tool (http://fragmentation-analyzer. googlecode.com) that makes it straightforward to analyze large MS/MS data sets for specific types of identified peptides, using a common set of peptide properties. This enables the detection of fragmentation pattern nuances related to specific instruments or due to the presence of post-translational modifications.

引用

收藏

页码：1087 / 1090

页数：4

相关论文

共 18 条

[1] Mass spectrometry-based proteomics [J].

Aebersold, R ;

Mann, M .

NATURE, 2003, 422 (6928) :198-207

[2] OMSSA Parser: An open-source library to parse and extract data from OMSSA MS/MS search results [J].

Barsnes, Harald ;

Huber, Steffen ;

Sickmann, Albert ;

Eidhammer, Ingvar ;

Martens, Lennart .

PROTEOMICS, 2009, 9 (14) :3772-3774

[3] Review - Mass spectrometry and protein analysis [J].

Domon, B ;

Aebersold, R .

SCIENCE, 2006, 312 (5771) :212-217

[4] Implementation and application of a versatile clustering tool for tandem mass spectrometry data [J].

Flikka, Kristian ;

Meukens, Jeroen ;

Helsensi, Kenny ;

Vandekerckhove, Joel ;

Eidhammer, Ingvar ;

Gevaert, Kris ;

Martens, Lennart .

PROTEOMICS, 2007, 7 (18) :3245-3258

[5] Open mass spectrometry search algorithm [J].

Geer, LY ;

Markey, SP ;

Kowalak, JA ;

Wagner, L ;

Xu, M ;

Maynard, DM ;

Yang, XY ;

Shi, WY ;

Bryant, SH .

JOURNAL OF PROTEOME RESEARCH, 2004, 3 (05) :958-964

[6] A la carte proteomics with an emphasis on gel-free techniques [J].

Gevaert, Kris ;

Van Damme, Petra ;

Ghesquiere, Bart ;

Impens, Francis ;

Martens, Lennart ;

Helsens, Kenny ;

Vandekerckhove, Joeel .

PROTEOMICS, 2007, 7 (16) :2698-2718

[7]

HELSENS K, 2010, PROTEOMICS IN PRESS, V10, DOI DOI 10.1002/PMIC.200900409

[8] MascotDatfile: An open-source library to fully parse and analyse MASCOT MS/MS search results [J].

Helsens, Kenny ;

Martens, Lennart ;

Vandekerckhove, Joel ;

Gevaert, Kris .

PROTEOMICS, 2007, 7 (03) :364-366

[9] NOVEL FRAGMENTATION PROCESS OF PEPTIDES BY COLLISION-INDUCED DECOMPOSITION IN A TANDEM MASS-SPECTROMETER - DIFFERENTIATION OF LEUCINE AND ISOLEUCINE [J].

JOHNSON, RS ;

MARTIN, SA ;

BIEMANN, K ;

STULTS, JT ;

WATSON, JT .

ANALYTICAL CHEMISTRY, 1987, 59 (21) :2621-2625

[10] Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification [J].

Klammer, Aaron A. ;

Reynolds, Sheila M. ;

Bilmes, Jeff A. ;

MacCoss, Michael J. ;

Noble, William Stafford .

BIOINFORMATICS, 2008, 24 (13) :I348-I356