Mass Spectrometry‐Based Proteomics Technologies to Define Endogenous Protein‐Protein Interactions and Their Applications to Cancer and Viral Infectious Diseases

Mass Spectrometry Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 9, 2025

An intricate network of protein assemblies and protein-protein interactions (PPIs) underlies nearly every biological process in living systems. The organization these cellular networks is highly dynamic intimately tied to the genomic proteomic landscapes a cell. Disruptions normal PPIs can impair functions contribute development human diseases. In recent years, targeting has emerged as an attractive strategy for drug discovery. Consequently, identification characterization endogenous PPIs-those occurring naturally under physiological conditions-has become crucial unraveling molecular mechanisms driving pathology laying groundwork novel diagnostics therapeutics. Owing numerous technological advancements, mass spectrometry (MS)-based proteomics transformed study at systems-level. This review focuses on approaches that enable physiologically relevant interactions, spanning complex-centric structure-centric analyses. Additionally, their applications define native contexts cancer viral infectious diseases highlighted.

Language: Английский

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In vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 28, 2025

ABSTRACT Cross-linking mass spectrometry has evolved as a powerful technique to study protein-protein interactions and provide structural information over the past decades. Low reaction efficiencies, complex matrices lead challenging system wide crosslink analysis. In this study, we improved streamlined an Azide-A-DSBSO based in vivo crosslinking workflow employing two orthogonal effective enrichment steps: Affinity size exclusion chromatography (SEC). Combined, they allow pulling of DSBSO containing peptides remove background linear well mono-linked peptides. We found that analysis single SEC fraction is yield ∼90% all crosslinks, which important whenever measurement time limited, sample throughput crucial. Our resulted more than 5000 crosslinks from K562 cells generated comprehensive PPI network whole nuclear extracts. From 393 within nucleus, 56 have not yet been reported STING database are representing valuable resource for investigating new molecular mechanisms complementary data future studies. further show, by applying extracts on lower abundant proteins showcase DEAD-box RNA helicase DDX39B predominantly expressed nucleus. indicates present monomeric dimeric form together with DDX39A analyzed.

Language: Английский

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Recent Progress in Mass Spectrometry-Based Liquid Biopsy for Cancer Detection and Analysis: A Comprehensive Review

TrAC Trends in Analytical Chemistry, Journal Year: 2025, Volume and Issue: unknown, P. 118291 - 118291

Published: May 1, 2025

Language: Английский

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Evaluating Imide-Based Mass Spectrometry-Cleavable Cross-Linkers for Structural Proteomics Studies

JACS Au, Journal Year: 2024, Volume and Issue: 4(8), P. 2936 - 2943

Published: July 16, 2024

Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates rapid and reliable identification of cross-links through the dissociation its group gas phase. In this study, we further advance capabilities by remodeling into an imide, thus introducing novel class cross-linkers. This modification preserves MS cleavability amide bond, granted two acyl groups imide function. The central nitrogen atom enables introduction affinity purification tags. Here, introduce disuccinimidyl disuccinic (DSSI) as prototype It features phosphonate handle for immobilized metal ion chromatography enrichment. We detail DSSI synthesis describe behavior solution phase while cross-linking proteins human cell lysates. are compared at same enrichment depth bridge these classes. validate mapping them high-resolution structures large assemblies. observed yield insights morphology intrinsically disordered their complexes. linker might spearhead MS-cleavable enrichable

Language: Английский

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Celebrating Women in Proteomics and Metabolomics

Journal of Proteome Research, Journal Year: 2024, Volume and Issue: 23(8), P. 2675 - 2679

Published: Aug. 2, 2024

Language: Английский

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