ArticleAnalytical chemistry2011
A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.
Article in Analytical chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat.Applied and environmental microbiology · 2020Article
- Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation.Environmental microbiology · 2020Article
- Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure.Journal of medical toxicology : official journal of the American College of Medical Toxicology · 2020Article
- New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells.The Analyst · 2019Review
- Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation.Nature microbiology · 2018Article
- High-Fat Diets Alter the Modulatory Effects of Xenobiotics on Cytochrome P450 Activities.Chemical research in toxicology · 2018Article
- Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142.Applied and environmental microbiology · 2016Article
- Hepatic Cytochrome P450 Activity, Abundance, and Expression Throughout Human Development.Drug metabolism and disposition: the biological fate of chemicals · 2016Article
- Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium.Frontiers in microbiology · 2016Article
- An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics.Journal of the American Society for Mass Spectrometry · 2015Article
- Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens.PLoS genetics · 2015Article
- Global analysis of Salmonella alternative sigma factor E on protein translation.Journal of proteome research · 2015Article
- Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea.BMC medical genomics · 2014Article
- Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics.Nature methods · 2014Article
- Proteomic analysis of saliva in HIV-positive heroin addicts reveals proteins correlated with cognition.PloS one · 2014Article
- Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch.PLoS biology · 2014Article
- Quantitative molecular phenotyping of gill remodeling in a cichlid fish responding to salinity stress.Molecular & cellular proteomics : MCP · 2013Article
- Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30.Molecular bioSystems · 2013Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.
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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.