ArticleAnalytical chemistry2023
High-Sensitivity Proteome-Scale Searches for Crosslinked Peptides Using CRIMP 2.0.
Article in Analytical chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Complete structures of the YenTc holotoxin prepore and pore reveal the evolutionary basis for chitinase incorporation into ABC toxins.Nature communications · 2025Article
- Click-linking: a cell-compatible protein crosslinking method based on click chemistry.Nature communications · 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
- Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure.Nature communications · 2024Article
- Rescuing error control in crosslinking mass spectrometry.Molecular systems biology · 2024Article
- Chemical cross-linking and mass spectrometry enabled systems-level structural biology.Current opinion in structural biology · 2024Review
- Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin.Analytical chemistry · 2024Article
- Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking.Mass spectrometry reviewsReview
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Crosslinking mass spectrometry (XL-MS) is a valuable technique for generating point-to-point distance measurements in protein space. However, cell-based XL-MS experiments require efficient software that can detect crosslinked peptides with sensitivity and controlled error rates. Many algorithms implement a filtering strategy designed to reduce the size of the database prior to mounting a search for crosslinks, but concern has been expressed over the possibility of reduced sensitivity using these strategies. We present a new scoring method that uses a rapid presearch method and a concept inspired by computer vision algorithms to resolve crosslinks from other conflicting reaction products. Searches of several curated crosslink datasets demonstrate high crosslink detection rates, and even the most complex proteome-level searches (using cleavable or noncleavable crosslinkers) can be completed efficiently on a conventional desktop computer. The detection of protein-protein interactions is increased twofold through the inclusion of compositional terms in the scoring equation. The combined functionality is made available as CRIMP 2.0 in the Mass Spec Studio.
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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.