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Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes.


ABSTRACT: Cross-linking analysis of protein complexes and structures by tandem mass spectrometry (MS/MS) has advantages in speed, sensitivity, specificity, and the capability of handling complicated protein assemblies. However, detection and accurate assignment of the cross-linked peptides are often challenging due to their low abundance and complicated fragmentation behavior in collision-induced dissociation (CID). To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked peptides, we developed a novel peptide enrichment strategy that utilizes a cross-linker with a cryptic thiol group and using beads modified with a photocleavable cross-linker. The functional cross-linkers were designed to react with the primary amino groups in proteins. Human serum albumin was used as a model protein to detect intra- and intermolecular cross-linkages. Use of this protein-free selective retrieval method eliminates the contamination that can result from avidin-biotin based retrieval systems and simplifies data analysis. These features may make the method suitable to investigate protein-protein interactions in biological samples.

SUBMITTER: Yan F 

PROVIDER: S-EPMC2765915 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes.

Yan Funing F   Che Fa-Yun FY   Rykunov Dmitry D   Nieves Edward E   Fiser Andras A   Weiss Louis M LM   Hogue Angeletti Ruth R  

Analytical chemistry 20090901 17


Cross-linking analysis of protein complexes and structures by tandem mass spectrometry (MS/MS) has advantages in speed, sensitivity, specificity, and the capability of handling complicated protein assemblies. However, detection and accurate assignment of the cross-linked peptides are often challenging due to their low abundance and complicated fragmentation behavior in collision-induced dissociation (CID). To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked pept  ...[more]

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2022-06-09 | PXD025099 | Pride