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Resolving protein interactions and complexes by affinity purification followed by label‐based quantitative mass spectrometry
Author(s) -
TrinkleMulcahy Laura
Publication year - 2012
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100438
Subject(s) - mass spectrometry , quantitative proteomics , chemistry , orbitrap , chromatography , quantitative analysis (chemistry) , resolution (logic) , immunoprecipitation , computational biology , tandem mass tag , proteomics , isobaric labeling , computer science , tandem mass spectrometry , biochemistry , protein mass spectrometry , biology , artificial intelligence , gene
Label‐based quantitative mass spectrometry analysis of affinity purified complexes, with its built‐in negative controls and relative ease of use, is an increasingly popular choice for defining protein–protein interactions and multiprotein complexes. This approach, which differentially labels proteins/peptides from two or more populations and combines them prior to analysis, permits direct comparison of a protein pulldown (e.g. affinity purified tagged protein) to that of a control pulldown (e.g. affinity purified tag alone) in a single mass spectrometry ( MS ) run, thus avoiding the variability inherent in separate runs. The use of quantitative techniques has been driven in large part by significant improvements in the resolution and sensitivity of high‐end mass spectrometers. Importantly, the availability of commercial reagents and open source identification/quantification software has made these powerful techniques accessible to nonspecialists. Benefits and drawbacks of the most popular labeling‐based approaches are discussed here, and key steps/strategies for the use of labeling in quantitative immunoprecipitation experiments detailed.