ArticleJournal of proteome research2010
TagRecon: high-throughput mutation identification through sequence tagging.
Article in Journal of proteome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 120 citations in OpenAlex.
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- Demystifying PTM Identification Using MODplus: Best Practices and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A modification-centric assessment tool for the performance of chemoproteomic probes.Nature chemical biology · 2022Article
- Improving the Genome Annotation ofCurrent genomics · 2021Article
- Functional Properties of Oligomeric and Monomeric Forms of Helicobacter pylori VacA Toxin.Infection and immunity · 2021Article
- Acceleration of age-induced proteolysis in the guinea pig lens nucleus by in vivo exposure to hyperbaric oxygen: A mass spectrometry analysis.Experimental eye research · 2021Article
- New insights into the mechanisms of age-related protein-protein crosslinking in the human lens.Experimental eye research · 2021Review
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics.Journal of proteome research · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Software Options for the Analysis of MS-Proteomic Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Biological Processes Highlighted inMicroorganisms · 2020Article
- Autophagic Proteome in TwoMicroorganisms · 2020Article
- Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions.Computational and structural biotechnology journal · 2020Review
- Cleavage C-terminal to Asp leads to covalent crosslinking of long-lived human proteins.Biochimica et biophysica acta. Proteins and proteomics · 2019Article
- DehydroalanylGly, a new post translational modification resulting from the breakdown of glutathione.Biochimica et biophysica acta. General subjects · 2018Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Shotgun proteomics produces collections of tandem mass spectra that contain all the data needed to identify mutated peptides from clinical samples. Identifying these sequence variations, however, has not been feasible with conventional database search strategies, which require exact matches between observed and expected sequences. Searching for mutations as mass shifts on specified residues through database search can incur significant performance penalties and generate substantial false positive rates. Here we describe TagRecon, an algorithm that leverages inferred sequence tags to identify unanticipated mutations in clinical proteomic data sets. TagRecon identifies unmodified peptides as sensitively as the related MyriMatch database search engine. In both LTQ and Orbitrap data sets, TagRecon outperformed state of the art software in recognizing sequence mismatches from data sets with known variants. We developed guidelines for filtering putative mutations from clinical samples, and we applied them in an analysis of cancer cell lines and an examination of colon tissue. Mutations were found in up to 6% of identified peptides, and only a small fraction corresponded to dbSNP entries. The RKO cell line, which is DNA mismatch repair deficient, yielded more mutant peptides than the mismatch repair proficient SW480 line. Analysis of colon cancer tumor and adjacent tissue revealed hydroxyproline modifications associated with extracellular matrix degradation. These results demonstrate the value of using sequence tagging algorithms to fully interrogate clinical proteomic data sets.
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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.