ArticleMolecular & cellular proteomics : MCP2010
DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.
Article in Molecular & cellular proteomics : MCP, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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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
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Elucidating regulatory processes of intense physical activity by multi-omics analysis.Military Medical Research · 2023Pooled it
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- Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity.Cell reports. Medicine · 2023Article
- TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis.Journal of proteome research · 2023Article
- The Key Role of Metal Adducts in the Differentiation of Phosphopeptide from Sulfopeptide Sequences by High-Resolution Mass Spectrometry.Analytical chemistry · 2022Article
- Assessment of TMT Labeling Efficiency in Large-Scale Quantitative Proteomics: The Critical Effect of Sample pH.ACS omega · 2021Article
- Parallel Multi-Omics in High-Risk Subjects for the Identification of Integrated Biomarker Signatures of Type 1 Diabetes.Biomolecules · 2021Article
- A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics.Journal of proteome research · 2021Review
- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Comprehensive Proteomics Analysis of Stressed Human Islets Identifies GDF15 as a Target for Type 1 Diabetes Intervention.Cell metabolism · 2020Article
- Joint learning improves protein abundance prediction in cancers.BMC biology · 2019Article
- The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes.Nature genetics · 2019Article
- Article
- Residual tissue repositories as a resource for population-based cancer proteomic studies.Clinical proteomics · 2018Article
- Changes of Protein Turnover in AgingMolecular & cellular proteomics : MCP · 2017Article
- Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.Journal of proteome research · 2017Article
- Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.Nature structural & molecular biology · 2017Article
- Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.Frontiers in microbiology · 2017Article
- Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica.BMC genomics · 2016Article
- An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics.Journal of the American Society for Mass Spectrometry · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and high throughput MS/MS fragmentation have become widely available in recent years, allowing for significantly better discrimination between true and false MS/MS peptide identifications by the application of a relatively narrow window for maximum allowable deviations of measured parent ion masses. To fully gain the advantage of highly accurate parent ion mass measurements, it is important to limit systematic mass measurement errors. Based on our previous studies of systematic biases in mass measurement errors, here, we have designed an algorithm and software tool that eliminates the systematic errors from the peptide ion masses in MS/MS data. We demonstrate that the elimination of the systematic mass measurement errors allows for the use of tighter criteria on the deviation of measured mass from theoretical monoisotopic peptide mass, resulting in a reduction of both false discovery and false negative rates of peptide identification. A software implementation of this algorithm called DtaRefinery reads a set of fragmentation spectra, searches for MS/MS peptide identifications using a FASTA file containing expected protein sequences, fits a regression model that can estimate systematic errors, and then corrects the parent ion mass entries by removing the estimated systematic error components. The output is a new file with fragmentation spectra with updated parent ion masses. The software is freely available.
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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.