ArticleMolecular & cellular proteomics : MCP2019
PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome.
Article in Molecular & cellular proteomics : MCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- PhosSight: A Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.Journal of proteome research · 2026Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- PgxSAVy: A tool for comprehensive evaluation of variant peptide quality in proteogenomics - catching the (un)usual suspects.Computational and structural biotechnology journal · 2024Article
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- A global view of the human post-translational modification landscape.The Biochemical journal · 2023Review
- The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I-Associated Peptides.Cancer immunology research · 2023Article
- A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra.Biophysics reports · 2022Article
- Many kinds of oxidized proteins are present more in the urine of the elderly.Clinical proteomics · 2022Article
- Systematic analysis of the lysine malonylome in Sanghuangporus sanghuang.BMC genomics · 2021Article
- caAtlas: An immunopeptidome atlas of human cancer.iScience · 2021Article
- Enhancing Open Modification Searches via a Combined Approach Facilitated by Ursgal.Journal of proteome research · 2021Article
- Review
- Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products.Natural product reports · 2021Review
- Global chemical modifications comparison of human plasma proteome from two different age groups.Scientific reports · 2020Article
- Transfer posterior error probability estimation for peptide identification.BMC bioinformatics · 2020Article
- Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search.Molecular & cellular proteomics : MCP · 2020Article
- PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.Journal of proteome research · 2019Article
- Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain.Mass spectrometry reviewsReview
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Authors and funding
7 authors.
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Abstract
The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. The performance of PTMiner was evaluated on three data sets, including simulated data, chemically synthesized peptide library data and modified-peptide spiked-in proteome data. The results showed that PTMiner can effectively control the PSM FDR and accurately localize the modification sites. At 1% real false localization rate (FLR), PTMiner localized 93%, 84 and 83% of the modification sites in the three data sets, respectively, far higher than two open search engines we used and an extended version of the Ascore localization algorithm. We then used PTMiner to analyze a draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown PTMs in the human proteome.
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