Development of Large-scale Cross-linking Mass Spectrometry

Abstract

<jats:p>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.</jats:p>

Cross‐linked peptide identification: A computational forest of algorithms

“…It is also much more difficult to reliably identify cross‐linked peptides, especially when one peptide is much shorter than the other; the fragmentation efficiency of the latter is usually inadequate as described above. Moreover, even when the shorter peptide produces enough fragment ions for identification, it is much more difficult to assign this peptide unambiguously as in the protein database, there might be several proteins that contain this peptide; a challenge which is of less significance when a cross‐linking experiment is performed on a purified protein complex …”

Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology

“…In recent years, in vitro XL-MS studies of protein complexes have produced enormous amounts of molecular details for understanding their architectures, functions and regulation 11,12,19,27,28,36,40–42,155,164,165 . However, it is more biologically relevant to perform in vivo cross-linking experiments as they can provide a more authentic map of protein-protein interactions (PPIs) occurring in native cellular environments 30 .…”

“…In recent years, significant technological advancements in XL-MS studies have dramatically propelled the field forward, enabling a wide range of applications in vitro and in vivo , not only at the level of protein complexes but also at the proteome scale. Several recent reviews have focused on specific aspects of XL-MS including reagent design 39 and applications 12,19,27,28,40–42 . This review offers an overview of recent developments in XL-MS studies especially during the last three years.…”

Systems vaccinology and big data in the vaccine development chain

“…5 However, the role of immunogens is currently studied in conjunction with other factors, such as adjuvants and antigen delivery, as these influence immune responses and induction of immunological memory that are key for vaccine ª 2018 The Authors. Immunology Published by John Wiley & Sons Ltd., Immunology, 156, [33][34][35][36][37][38][39][40][41][42][43][44][45][46] efficacy. Systems vaccinology addresses these aspects in order to understand why some vaccines function properly whereas other vaccines do not.…”

“…A new class of MS-cleavable cross-linking reagents has a great potential in interactomics. [34][35][36] Like all other cross-linking reagents, these compounds stabilize transient protein-protein interactions by the formation of covalent bonds under physiological conditions. But they also allow for the unambiguous identification of the spatially distributed peptides of the interacting proteins, based on the presence of characteristic reporter ions in the mass spectra that are representative for intramolecular or intermolecular cross-links.…”