ArticleJournal of proteome research2007
Informatics strategies for large-scale novel cross-linking analysis.
Article in Journal of proteome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 51 citations in OpenAlex.
- In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.Chemical reviews · 2022Review
- Applications and advancements of FT-ICR-MS for interactome studies.Mass spectrometry reviews · 2022Review
- Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions.Computational and structural biotechnology journal · 2020Review
- Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes.Nature protocols · 2019Article
- The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies.Journal of the American Society for Mass Spectrometry · 2019Article
- Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology.Nature structural & molecular biology · 2018Review
- Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry.Trends in biochemical sciences · 2018Review
- CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.Journal of proteome research · 2017Article
- In vivo protein interaction network analysis reveals porin-localized antibiotic inactivation in Acinetobacter baumannii strain AB5075.Nature communications · 2016Article
- Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection.Expert review of proteomics · 2016Review
- Protein Structural Analysis via Mass Spectrometry-Based Proteomics.Advances in experimental medicine and biology · 2016Review
- Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.Protein science : a publication of the Protein Society · 2015Review
- Kojak: efficient analysis of chemically cross-linked protein complexes.Journal of proteome research · 2015Article
- Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry.Structure (London, England : 1993) · 2015Article
- Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze.Journal of structural and functional genomics · 2013Review
- Protein interactions, post-translational modifications and topologies in human cells.Molecular & cellular proteomics : MCP · 2013Article
- In vivo protein interaction network identified with a novel real-time cross-linked peptide identification strategy.Journal of proteome research · 2013Article
- Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions.Journal of proteome research · 2012Article
- Review
- In vivo application of photocleavable protein interaction reporter technology.Journal of proteome research · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The detection of protein interactions in biological systems represents a significant challenge for today's technology. Chemical cross-linking provides the potential to impart new chemical bonds in a complex system that result in mass changes in a set of tryptic peptides detected by mass spectrometry. However, system complexity and cross-linking product heterogeneity have precluded widespread chemical cross-linking use for large-scale identification of protein-protein interactions. The development of mass spectrometry identifiable cross-linkers called protein interaction reporters (PIRs) has enabled on-cell chemical cross-linking experiments with product type differentiation. However, the complex datasets resultant from PIR experiments demand new informatics capabilities to allow interpretation. This manuscript details our efforts to develop such capabilities and describes the program X-links, which allows PIR product type differentiation. Furthermore, we also present the results from Monte Carlo simulation of PIR-type experiments to provide false discovery rate estimates for the PIR product type identification through observed precursor and released peptide masses. Our simulations also provide peptide identification calculations based on accurate masses and database complexity that can provide an estimation of false discovery rates for peptide identification. Overall, the calculations show a low rate of false discovery of PIR product types due to random mass matching of approximately 12% with 10 ppm mass measurement accuracy and spectral complexity resulting from 100 peptides. In addition, consideration of a reduced database resulting from stage 1 analysis of Shewanella oneidensis MR-1 containing 367 proteins resulted in a significant reduction of expected identification false discovery rate estimation compared to that from the entire Shewanella oneidensis MR-1 proteome.
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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.