ArticleChemical research in toxicology2011
Sequence tagging reveals unexpected modifications in toxicoproteomics.
Article in Chemical research in toxicology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Demystifying PTM Identification Using MODplus: Best Practices and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells.Molecular & cellular proteomics : MCP · 2017Article
- MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.Nature methods · 2017Article
- Biomonitoring Human Albumin Adducts: The Past, the Present, and the Future.Chemical research in toxicology · 2017Article
- Release of skeletal muscle peptide fragments identifies individual proteins degraded during insulin deprivation in type 1 diabetic humans and mice.American journal of physiology. Endocrinology and metabolism · 2016Article
- The SEQUEST family tree.Journal of the American Society for Mass Spectrometry · 2015Article
- Current peptidomics: applications, purification, identification, quantification, and functional analysis.Proteomics · 2015Review
- Fast and accurate database searches with MS-GF+Percolator.Journal of proteome research · 2014Article
- Protein analysis by shotgun/bottom-up proteomics.Chemical reviews · 2013Review
- Informatics of protein and posttranslational modification detection via shotgun proteomics.Methods in molecular biology (Clifton, N.J.) · 2013Article
- Chronic caloric restriction preserves mitochondrial function in senescence without increasing mitochondrial biogenesis.Cell metabolism · 2012Article
- Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach.Molecular & cellular proteomics : MCP · 2012Article
- Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.Journal of proteome research · 2012Article
- Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.Current protocols in bioinformatics · 2012Article
- Obesity and altered glucose metabolism impact HDL composition in CETP transgenic mice: a role for ovarian hormones.Journal of lipid research · 2012Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Toxicoproteomic samples are rich in posttranslational modifications (PTMs) of proteins. Identifying these modifications via standard database searching can incur significant performance penalties. Here, we describe the latest developments in TagRecon, an algorithm that leverages inferred sequence tags to identify modified peptides in toxicoproteomic data sets. TagRecon identifies known modifications more effectively than the MyriMatch database search engine. TagRecon outperformed state of the art software in recognizing unanticipated modifications from LTQ, Orbitrap, and QTOF data sets. We developed user-friendly software for detecting persistent mass shifts from samples. We follow a three-step strategy for detecting unanticipated PTMs in samples. First, we identify the proteins present in the sample with a standard database search. Next, identified proteins are interrogated for unexpected PTMs with a sequence tag-based search. Finally, additional evidence is gathered for the detected mass shifts with a refinement search. Application of this technology on toxicoproteomic data sets revealed unintended cross-reactions between proteins and sample processing reagents. Twenty-five proteins in rat liver showed signs of oxidative stress when exposed to potentially toxic drugs. These results demonstrate the value of mining toxicoproteomic data sets for modifications.
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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.