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thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files

Niklaas Colaert UGent, Harald Barsnes, Marc Vaudel, Kenny Helsens UGent, Evy Timmerman UGent, Albert Sickmann, Kris Gevaert UGent and Lennart Martens UGent (2011) JOURNAL OF PROTEOME RESEARCH. 10(8). p.3840-3843
abstract
The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
TANDEM, TOOL, PEPTIDE, SOFTWARE, IDENTIFICATION, QUANTIFICATION, MASS-SPECTROMETRY DATA, mass spectrometry, proteomics, bioinformatics
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
10
issue
8
pages
3840 - 3843
Web of Science type
Article
Web of Science id
000293487900048
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.113 (2011)
JCR rank
10/72 (2011)
JCR quartile
1 (2011)
ISSN
1535-3893
DOI
10.1021/pr2005154
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1906830
handle
http://hdl.handle.net/1854/LU-1906830
date created
2011-09-22 14:27:28
date last changed
2013-02-27 09:11:21
@article{1906830,
  abstract     = {The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.},
  author       = {Colaert, Niklaas and Barsnes, Harald and Vaudel, Marc and Helsens, Kenny and Timmerman, Evy and Sickmann, Albert and Gevaert, Kris and Martens, Lennart},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {TANDEM,TOOL,PEPTIDE,SOFTWARE,IDENTIFICATION,QUANTIFICATION,MASS-SPECTROMETRY DATA,mass spectrometry,proteomics,bioinformatics},
  language     = {eng},
  number       = {8},
  pages        = {3840--3843},
  title        = {thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files},
  url          = {http://dx.doi.org/10.1021/pr2005154},
  volume       = {10},
  year         = {2011},
}

Chicago
Colaert, Niklaas, Harald Barsnes, Marc Vaudel, Kenny Helsens, Evy Timmerman, Albert Sickmann, Kris Gevaert, and Lennart Martens. 2011. “Thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer Msf Files.” Journal of Proteome Research 10 (8): 3840–3843.
APA
Colaert, N., Barsnes, H., Vaudel, M., Helsens, K., Timmerman, E., Sickmann, A., Gevaert, K., et al. (2011). thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. JOURNAL OF PROTEOME RESEARCH, 10(8), 3840–3843.
Vancouver
1.
Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, et al. thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files. JOURNAL OF PROTEOME RESEARCH. 2011;10(8):3840–3.
MLA
Colaert, Niklaas, Harald Barsnes, Marc Vaudel, et al. “Thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer Msf Files.” JOURNAL OF PROTEOME RESEARCH 10.8 (2011): 3840–3843. Print.