Abstract
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large data sets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
Highlights
Cross-linking Mass Spectrometry and the Analysis of Protein Complexes and Protein-Protein Interactions—Chemical cross-linking in combination with mass spectrometry is a technology that has been used for over a decade to reveal the topology of protein complexes and protein-protein interactions [1]
The constant improvement of the Cross-linking Mass Spectrometry (CLMS) technology over the past decade has resulted a powerful tool to study the structure of protein complexes
The technology has so far delivered data, which helped to understand the function of key multiprotein complexes in human body
Summary
Cross-linking Mass Spectrometry and the Analysis of Protein Complexes and Protein-Protein Interactions—Chemical cross-linking in combination with mass spectrometry is a technology that has been used for over a decade to reveal the topology of protein complexes and protein-protein interactions [1]. Fragmentation can occur at the peptide amide bond adjacent to the cross-linked residues, generating ions containing parts of both peptides and the cross-linker (Fig. 2 y4␣, y3, b2␣, b2). The software XlinkX is designed to work only with S-S-cleavable cross-linkers and can both determine the accurate precursor masses and obtain the sequence of the two linked peptides combining the information from MS, MS2, and MS3 [4].
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