ArticleJournal of proteome research2020
Crystal-C: A Computational Tool for Refinement of Open Search Results.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Trifluoroacetate mediated reduction of atherosclerosis in mice.Nature communications · 2026Article
- Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.Nature chemistry · 2026Article
- Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona.Nature communications · 2026Article
- A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.Journal of proteome research · 2026Article
- Profiling the proteome-wide selectivity of diverse electrophiles.Nature chemistry · 2025Article
- A transcriptomic, proteomic, and functional genetic atlas dissects neurofibromin function in the peripheral nervous system.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Fecal proteomics of wild capuchins reveals impacts of season, diet, age, and, sex on gut physiology.bioRxiv : the preprint server for biology · 2025Article
- Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq.Nature biotechnology · 2025Article
- Total syntheses of cyclohelminthol I-IV reveal a new cysteine-selective covalent reactive group.Chemical science · 2025Article
- PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins.Journal of proteome research · 2025Article
- Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.The EMBO journal · 2025Article
- Article
- Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB.Communications biology · 2024Article
- deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets.Bioinformatics (Oxford, England) · 2024Article
- Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker.Communications biology · 2024Article
- Fitness Effects of Phenotypic Mutations at Proteome-Scale Reveal Optimality of Translation Machinery.Molecular biology and evolution · 2024Article
- Improved deconvolution of natural products' protein targets using diagnostic ions from chemical proteomics linkers.Beilstein journal of organic chemistry · 2024Review
- Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity.bioRxiv : the preprint server for biology · 2023Article
- A region-resolved proteomic map of the human brain enabled by high-throughput proteomics.The EMBO journal · 2023Article
- Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides.Nature communications · 2023Article
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Authors and funding
6 authors.
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Abstract
Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational modifications. With the emergence of fast database search tools such as MSFragger, the approach of enlarging precursor mass tolerances during the search (termed "open search") has been increasingly used for comprehensive characterization of post-translational and chemical modifications of protein samples. However, not all mass shifts detected using the open search strategy represent true modifications, as artifacts exist from sources such as unaccounted missed cleavages or peptide co-fragmentation (chimeric MS/MS spectra). Here, we present Crystal-C, a computational tool that detects and removes such artifacts from open search results. Our analysis using Crystal-C shows that, in a typical shotgun proteomics data set, the number of such observations is relatively small. Nevertheless, removing these artifacts helps to simplify the interpretation of the mass shift histograms, which in turn should improve the ability of open search-based tools to detect potentially interesting mass shifts for follow-up investigation.
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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.