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J Am Soc Mass Spectrom. 2013 Mar;24(3):444-9. doi: 10.1007/s13361-012-0565-x. Epub 2013 Feb 20.

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking.

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1
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

Abstract

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.

PMID:
23423792
PMCID:
PMC3594340
DOI:
10.1007/s13361-012-0565-x
[Indexed for MEDLINE]
Free PMC Article
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