Quantitative interactome analysis with chemical cross-linking and mass spectrometry

Wippel, Helisa Helena; Chavez, Juan D.; Tang, Xiaoting; Bruce, James E.

doi:10.1016/j.cbpa.2021.06.011

Cited by 31 publications

(32 citation statements)

References 58 publications

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“…51 The identification and validation of cross-links found in this study were performed manually, and the first dedicated software for an automated quantification of isotope-labeled cross-linked peptides was introduced at roughly the same time. 50 Since then, a number of software tools have been developed or integrated for QXL-MS and become available, 180 particularly for noncleavable crosslinkers. In the case of MS-cleavable cross-linkers, the bioinformatics resources are poorly developed; consequently, the application of QXL-MS in system-wide studies is still limited.…”

Section: Quantitative Cross-linkingmentioning

confidence: 99%

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

Piersimoni¹,

Kastritis

Arlt³

et al. 2021

Chem. Rev.

154

103

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Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein–protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.

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Section: Quantitative Cross-linkingmentioning

confidence: 99%

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

Piersimoni¹,

Kastritis

Arlt³

et al. 2021

Chem. Rev.

154

103

View full text Add to dashboard Cite

show abstract

“…In recent years, there have been studies designed to perform quantitative XL-MS (QXL-MS) [18,21,26,27 which applied MS technique to quantify proteins at single-cell level [29]. Another study introduced a streamlined workflow to apply MS for single-cell proteomic analysis [30].…”

Section: Quantitative Techniques Provide Quantification Information Ofmentioning

confidence: 99%

Protein‐protein interaction networks as miners of biological discovery

Wang

Lü

et al. 2022

Proteomics

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Protein-protein interactions (PPIs) form the basis of a myriad of biological pathways and mechanism, such as the formation of protein complexes or the components of signaling cascades. Here, we reviewed experimental methods for identifying PPI pairs, including yeast two-hybrid (Y2H), mass spectrometry (MS), co-localization, and coimmunoprecipitation. Furthermore, a range of computational methods leveraging biochemical properties, evolution history, protein structures and more have enabled identification of additional PPIs. Given the wealth of known PPIs, we reviewed important network methods to construct and analyze networks of PPIs. These methods aid biological discovery through identifying hub genes and dynamic changes in the network, and have been thoroughly applied in various fields of biological research. Lastly, we discussed the challenges and future direction of research utilizing the power of PPI networks.

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“…Benefiting from the rapid development of technology during the 21st century, some classical technologies have helped to further revolutionize proteomics. For example, 2D-PAGE and MS have been developed into techniques such as difference-gel 2D-electrophoresis ( Larbi and Jefferies, 2009 ), surface-enhanced laser desorption/ionization time of flight (SELDI-TOF) MS ( Marcos et al, 2013 ), quantitative chemical cross-linking with MS ( Wippel et al, 2021 ), and immunodepletion techniques for “low-abundance” protein determination ( Liu et al, 2021b ). Moreover, “protein chips” have been designed and combined with MS approaches for the specific analysis of selected proteins ( Zhou et al, 2001 ).…”

Section: Proteomics Research Approachesmentioning

confidence: 99%

Proteomics in Biomarker Discovery for Tuberculosis: Current Status and Future Perspectives

et al. 2022

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Tuberculosis (TB) continues to threaten many peoples’ health worldwide, regardless of their country of residence or age. The current diagnosis of TB still uses mainly traditional, time-consuming, and/or culture-based techniques. Efforts have focused on discovering new biomarkers with higher efficiency and accuracy for TB diagnosis. Proteomics—the systematic study of protein diversity—is being applied to the discovery of novel protein biomarkers for different types of diseases. Mass spectrometry (MS) technology plays a revolutionary role in proteomics, and its applicability benefits from the development of other technologies, such as matrix-based and immune-based methods. MS and derivative strategies continuously contribute to disease-related discoveries, and some promising proteomic biomarkers for efficient TB diagnosis have been identified, but challenges still exist. For example, there are discrepancies in the biomarkers identified among different reports and the diagnostic accuracy of clinically applied proteomic biomarkers. The present review summarizes the current status and future perspectives of proteomics in the field of TB biomarker discovery and aims to elicit more promising findings for rapid and accurate TB diagnosis.

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Quantitative interactome analysis with chemical cross-linking and mass spectrometry

Cited by 31 publications

References 58 publications

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

Protein‐protein interaction networks as miners of biological discovery

Proteomics in Biomarker Discovery for Tuberculosis: Current Status and Future Perspectives

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