title: Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.
abstract: 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 5 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.
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98103, USA. edeutsch@systemsbiology.org
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030562:Databases, Protein; D001330:Electronic Data Processing / Q000379:methods*; D006801:Humans; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D017150:Public Sector; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D054928:Validation Studies as Topic
chemical_list: D020543:Proteome