Relative and Absolute Quantitation in Mass Spectrometry–Based Proteomics
- 12 June 2018
- journal article
- research article
- Published by Annual Reviews in Annual Review of Analytical Chemistry
- Vol. 11 (1), 49-77
- https://doi.org/10.1146/annurev-anchem-061516-045357
Abstract
Mass spectrometry–based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label–based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling–based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.Keywords
This publication has 156 references indexed in Scilit:
- Advancing the sensitivity of selected reaction monitoring‐based targeted quantitative proteomicsProteomics, 2012
- MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomicsNature Methods, 2011
- Global quantification of mammalian gene expression controlNature, 2011
- More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MSJournal of Proteome Research, 2011
- Improved LC−MS/MS Spectral Counting Statistics by Recovering Low-Scoring Spectra Matched to Confidently Identified Peptide SequencesJournal of Proteome Research, 2010
- N,N-Dimethyl Leucines as Novel Isobaric Tandem Mass Tags for Quantitative Proteomics and PeptidomicsAnalytical Chemistry, 2010
- FLEXIQuant: A Novel Tool for the Absolute Quantification of Proteins, and the Simultaneous Identification and Quantification of Potentially Modified PeptidesJournal of Proteome Research, 2009
- Selected reaction monitoring for quantitative proteomics: a tutorialMolecular Systems Biology, 2008
- 8‐Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's diseaseProteomics, 2007
- Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networksProceedings of the National Academy of Sciences of the United States of America, 2007