ArticleMolecular & cellular proteomics : MCP2011
Modification site localization scoring integrated into a search engine.
Article in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
What it found
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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
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis.Molecular & cellular proteomics : MCP · 2021Pooled it
- PhosSight: A Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- Finding coexisting combinations of posttranslational modifications with HomMTM spectra.Briefings in bioinformatics · 2025Article
- Advancements in Global Phosphoproteomics Profiling: Overcoming Challenges in Sensitivity and Quantification.Proteomics · 2025Review
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Deep Learning Prediction Boosts Phosphoproteomics-Based Discoveries Through Improved Phosphopeptide Identification.Molecular & cellular proteomics : MCP · 2024Article
- Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics.Nature communications · 2023Article
- DeepFLR facilitates false localization rate control in phosphoproteomics.Nature communications · 2023Article
- Principles of phosphoproteomics and applications in cancer research.The Biochemical journal · 2023Article
- Measuring the multifaceted roles of mucin-domain glycoproteins in cancer.Advances in cancer research · 2023Review
- Transthyretin proteoforms of intraocular origin in human subretinal fluid.Experimental eye research · 2022Article
- Review
- Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.Journal of proteome research · 2022Article
- Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.Nature methods · 2021Article
- The RAS GTPase RIT1 compromises mitotic fidelity through spindle assembly checkpoint suppression.Current biology : CB · 2021Article
- Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging.Expert review of proteomics · 2021Review
- The Hitchhiker's guide to glycoproteomics.Biochemical Society transactions · 2021Review
- Advances in quantitative high-throughput phosphoproteomics with sample multiplexing.Proteomics · 2021Review
- Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.Molecular & cellular proteomics : MCP · 2021Review
5 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
3 authors.
Funding
Abstract
Large proteomic data sets identifying hundreds or thousands of modified peptides are becoming increasingly common in the literature. Several methods for assessing the reliability of peptide identifications both at the individual peptide or data set level have become established. However, tools for measuring the confidence of modification site assignments are sparse and are not often employed. A few tools for estimating phosphorylation site assignment reliabilities have been developed, but these are not integral to a search engine, so require a particular search engine output for a second step of processing. They may also require use of a particular fragmentation method and are mostly only applicable for phosphorylation analysis, rather than post-translational modifications analysis in general. In this study, we present the performance of site assignment scoring that is directly integrated into the search engine Protein Prospector, which allows site assignment reliability to be automatically reported for all modifications present in an identified peptide. It clearly indicates when a site assignment is ambiguous (and if so, between which residues), and reports an assignment score that can be translated into a reliability measure for individual site assignments.
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Registered trials
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