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Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):29-41. doi: 10.1016/j.bbapap.2013.03.026. Epub 2013 Apr 6.

Data processing methods and quality control strategies for label-free LC-MS protein quantification.

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Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden.


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.


LC–MS; Label free; Protein quantification; Quality control; Quantitative proteomics; Selected reaction monitoring

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