ArticleJournal of the American Society for Mass Spectrometry2012
StavroX--a software for analyzing crosslinked products in protein interaction studies.
Article in Journal of the American Society for Mass Spectrometry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 185 papers.
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Who cites it
185 citing papers in PubMed, 352 citations in OpenAlex.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and rubredoxin-ENH1 to the stromal side of photosystem II in higher plants.The Journal of biological chemistry · 2026Article
- XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry.Nature communications · 2026Article
- Selection of short Gadd45β-binding peptides through a synergistic computational and biophysical approach.Protein science : a publication of the Protein Society · 2025Article
- Conserved hydrophilic checkpoints tune FocA-mediated formate:HNature communications · 2025Article
- Structural Basis for a Scaffolding Role of the COM Domain in Nonribosomal Peptide Synthetases.Angewandte Chemie (International ed. in English) · 2025Article
- The Actin-Binding Prolyl-Isomerase Par17 Sustains Its Substrate Selectivity by Interdomain Allostery.Proteins · 2025Article
- A substrate-interacting region of Parkin directs ubiquitination of the mitochondrial GTPase Miro1.The Journal of cell biology · 2025Article
- An intrinsically disordered region of Ubp10 regulates its binding and activity on ubiquitinated histone substrates.Protein science : a publication of the Protein Society · 2025Article
- The structure of FCGBP is formed as a disulfide-mediated homodimer between its C-terminal domains.The FEBS journal · 2025Article
- Physicochemical quality assessment of four asparaginases.PloS one · 2025Article
- Cross-Linking Mass Spectrometry to Capture Protein Network Dynamics of Cell Membranome.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid.Journal of proteome research · 2024Article
- Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping.Nature communications · 2024Article
- Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry.Advances in experimental medicine and biology · 2024Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
- Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo.Analytical chemistry · 2023Article
- The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase.Nature communications · 2023Article
- High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.Analytical chemistry · 2023Article
125 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.
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