A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments

Journal Article · Fri Feb 01 04:00:00 EST 2013 · Proteomics, 13(3-4):493-503

DOI:https://doi.org/10.1002/pmic.201200269· OSTI ID:1072870

Matzke, Melissa M; Brown, Joseph N; Gritsenko, Marina A; Metz, Thomas O; Pounds, Joel G; Rodland, Karin D; Shukla, Anil K; Smith, Richard D; Waters, Katrina M; McDermott, Jason E; Webb-Robertson, Bobbie-Jo M

Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1072870
• Report Number(s): PNNL-SA-88866; 16303; 16303a
• Journal Information: Proteomics, 13(3-4):493-503, Journal Name: Proteomics, 13(3-4):493-503
• Country of Publication: United States
• Language: English

Related Subjects

Environmental Molecular Sciences Laboratory
Label-free
Peak intensity
Protein quantification
Relative