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Physiol. Genomics (January 22, 2008). doi:10.1152/physiolgenomics.00298.2007
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Submitted on December 20, 2007
Accepted on January 18, 2008

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics

Eric W Deutsch1*, Henry Lam1, and Ruedi Aebersold1

1 Institute for Systems Biology, Seattle, Washington, United States

* To whom correspondence should be addressed. E-mail: edeutsch{at}systemsbiology.org.

Data processing is a central and critical component of a successful proteomics experiment, and is often the most time-consuming step. There have been considerable advances in the field of proteomics informatics in the past five years, spurred mainly by free and open source software tools. Along with the gains afforded by new software, the benefits of making raw data and processed results freely available to the community in data repositories are finally in evidence. In this review, we provide an overview of the general analysis approaches, software tools, and repositories that are enabling successful proteomics research via tandem mass spectrometry.




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