SpringerProtocols: Abstract: Using Stable Isotope Tagging and Mass Spectrometry to Characterize Protein Complexes and to Detect Changes in Their Composition

Using Stable Isotope Tagging and Mass Spectrometry to Characterize Protein Complexes and to Detect Changes in Their Composition

By: Jeffrey A. Ranish², Marjorie Brand³, Ruedi Aebersold^{4 5}

Abstract

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One of the primary goals of proteomics is the description of the composition, dynamics, and connections of the multiprotein modules that catalyze a wide range of biological functions in cells. Mass spectrometry (MS) has proven to be an extremely powerful tool for characterizing the composition of purified complexes. However, because MS is not a quantitative technique, the usefulness of the data is limited. For example, without quantitative measurements, it is difficult to detect dynamic changes in complex composition, and it can be difficult to distinguish bona fide complex components from nonspecifically copurifying proteins. In this chapter, we describe a strategy for characterizing the composition of protein complexes and their dynamic changes in composition by combining affinity purification approaches with stable isotope tagging and MS. The use of software tools for statistical analysis of the data is also described.

Affiliation(s): (2) Institute for Systems Biology, Seattle, WA
(3) Ottawa Health Research Institute, Molecular Medicine Program, Ottawa, Ontario, Canada
(4) Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
(5) Faculty of Science, University of Zurich, Zurich, Switzerland

Book Title: Quantitative Proteomics by Mass Spectrometry

Series: Methods in Molecular Biology | Volume: 359 | Pub. Date: Feb-05-2007 | Page Range: 17-35 | DOI: 10.1007/978-1-59745-255-7_2

Subject: Biochemistry

Key Words: Mass spectrometry - stable isotope tagging - ICAT reagents - quantification - protein complex - dynamics - affinity purification - SEQUEST - Peptide Prophet - Protein Prophet - ASAPratio

References

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