ArticleMolecular & cellular proteomics : MCP2012
Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography.
Article in Molecular & cellular proteomics : MCP, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
161 citing papers in PubMed, 318 citations in OpenAlex.
- FHL2 production enabled new insight into its flexibility and unexpected binding stoichiometry with β-catenin.Journal of structural biology: X · 2026Article
- Mapping Interaction of Assembly Factor Rpn14 With the Proteasome Base Reveals a Bipartite Interface and Implies Ordered Remodeling of Intersubunit Contacts During Proteasome Biogenesis.Journal of molecular biology · 2026Article
- Structure of cytoplasmic RNA polymerase II.Nature communications · 2026Article
- Structural mass spectrometry techniques for characterisation of plant and algal proteins.The Plant journal : for cell and molecular biology · 2026Review
- Histone 3 lysine 9 dimethylation by the G9a-GLP heterodimer requires intranucleosomal product reading.bioRxiv : the preprint server for biology · 2026Article
- Breaking barriers in crosslinking mass spectrometry with enhanced throughput and sensitivity using Orbitrap Astral.Nature communications · 2025Article
- In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.Communications chemistry · 2025Article
- Trioxane-based MS-cleavable cross-linking mass spectrometry for profiling multimeric interactions of cellular networks.Nature communications · 2025Article
- Identification of a direct interaction between the Fab domains of IgG antibodies and human FcRn upon IgG-FcRn complex formation.Communications biology · 2025Article
- A highly sensitive protein-RNA cross-linking mass spectrometry workflow with enhanced structural modeling potential.Nucleic acids research · 2025Article
- Structure of the nucleosome-bound human BCL7A.Nucleic acids research · 2025Article
- Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.Cell · 2024Article
- Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system.Journal of proteins and proteomics · 2024Article
- Structure of the human 20S U5 snRNP.Nature structural & molecular biology · 2024Article
- Article
- Structural basis for RAD18 regulation by MAGEA4 and its implications for RING ubiquitin ligase binding by MAGE family proteins.The EMBO journal · 2024Article
- Multidimensional Cross-Linking and Real-Time Informatics for Multiprotein Interaction Studies.Journal of proteome research · 2024Article
- Characterization of β-Barrel Outer Membrane Proteins and Their Interactions with Chaperones by Chemical-Crosslinking Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Cross-linking mass spectrometric analysis of the endogenous TREX complex fromRNA (New York, N.Y.) · 2023Article
- Higher-Order Structural Organization of the Mitochondrial Proteome Charted by In Situ Cross-Linking Mass Spectrometry.Molecular & cellular proteomics : MCP · 2023Article
101 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.