Journal
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
Volume 1844, Issue 1, Pages 29-41Publisher
ELSEVIER
DOI: 10.1016/j.bbapap.2013.03.026
Keywords
Protein quantification; Quantitative proteomics; Quality control; Label free; LC-MS; Selected reaction monitoring
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Funding
- Swedish Foundation for Strategic Research [RBb08-0006, SSF-FFL4]
- Swedish Research Council (BILS) [2007-5188, 2008-3356]
- Crafoord Foundation [20100892]
- Swedish Foundation for Strategic Research (SSF) [RBb08-0006] Funding Source: Swedish Foundation for Strategic Research (SSF)
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Protein quantification using different LC-MS techniques is becoming a standard practice. However, with a multitude of experimental setups to choose from, as well as a wide array of software solutions for subsequent data processing, it is non-trivial to select the most appropriate workflow for a given biological question. In this review, we highlight different issues that need to be addressed by software for quantitative LC-MS experiments and describe different approaches that are available. With focus on label-free quantification, examples are discussed both for LC-MS/MS and LC-SRM data processing. We further elaborate on current quality control methodology for performing accurate protein quantification experiments. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V. All rights reserved.
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