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

作者：Sandin Marianne; Teleman Johan; Malmstrom Johan; Levander Fredrik^*

来源：Biochimica et Biophysica Acta-Proteins and Proteomics, 2014, 1844(1): 29-41.

DOI：10.1016/j.bbapap.2013.03.026

• Protein quantification
• Quantitative proteomics
• Quality control
• Label free
• LC-MS
• Selected reaction monitoring

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.

• 出版日期2014-1