Skip Navigation



Bioinformatics Advance Access published online on August 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth460
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/18/3628    most recent
bth460v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Samuelsson, J.
Right arrow Articles by Rögnvaldsson, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Samuelsson, J.
Right arrow Articles by Rögnvaldsson, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received February 20, 2004
Revised July 26, 2004
Accepted July 27, 2004

Article

Modular, Scriptable, and Automated Analysis Tools for High-Throughput Peptide Mass Fingerprinting

Jim Samuelsson 1, Daniel Dalevi 2, Fredrik Levander 3, Thorsteinn Rögnvaldsson 4*

1 Genedata GmbH, Lena-Christ-Str. 50, 82152 Martinsried, Germany
2 Computing Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
3 Dept. of Protein Technology, Lund University, Sölvegatan 33A, SE-223 62 Lund, Sweden
4 School of Information Science, Computer and Electronic Engineering, Halmstad University, Box 823, SE-301 18 Halmstad, Sweden

* To whom correspondence should be addressed. E-mail: denni{at}ide.hh.se.


  Abstract

A set of new algorithms and software tools for automatic protein identification using peptide mass fingerprinting is presented. The software is automatic, fast and modular to suit different laboratory needs, and it can be operated either via a Java user interface or called from within scripts. The software modules do peak extraction, peak filtering, and protein database matching, and communicate via XML. Individual modules can therefore easily be replaced with other software if desired, and all intermediate results are available to the user. The algorithms are designed to operate without human intervention and contain several novel approaches. The performance and capabilities of the software is illustrated on spectra from different mass spectrometer manufacturers, and the factors influencing successful identification are discussed and quantified.

Motivation: Protein identification with mass spectrometric methods is a key step in modern proteomics studies. Some tools are available today for doing different steps in the analysis. Only a few commercial systems integrate all the steps in the analysis, often for only one vendor's hardware, and the details of these systems are not public.

Results: A complete system for doing protein identification with peptide mass fingerprints is presented, including everything from peak picking to matching the database protein. The details of the different algorithms are disclosed so that academic researchers can have full control of their tools.

Additional material: Details of the algorithms are described in supporting information available from the Halmstad University website www.hh.se/sta./bioinf/.

Availability: The described software tools are available from the Halmstad University website www.hh.se/sta./bioinf/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
I. A. Bogdan, J. Rivers, R. J. Beynon, and D. Coca
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting
Bioinformatics, July 1, 2008; 24(13): 1498 - 1502.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
I. Bogdan, D. Coca, J. Rivers, and R. J Beynon
Hardware acceleration of processing of mass spectrometric data for proteomics
Bioinformatics, March 15, 2007; 23(6): 724 - 731.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
O. Kohlbacher, K. Reinert, C. Gropl, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, and M. Sturm
TOPP--the OpenMS proteomics pipeline
Bioinformatics, January 15, 2007; 23(2): e191 - e197.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.