ArticleBMC bioinformatics2011
The proteogenomic mapping tool.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The trial behind it
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
18 citing papers in PubMed.
- An overview of technologies for MS-based proteomics-centric multi-omics.Expert review of proteomics · 2022Article
- Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing.International journal of molecular sciences · 2021Article
- Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues.Frontiers in cell and developmental biology · 2021Article
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.BMC genomics · 2019Article
- A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.Journal of visualized experiments : JoVE · 2018Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.Cell systems · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach.The Journal of general virology · 2016Article
- PGx: Putting Peptides to BED.Journal of proteome research · 2016Article
- A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.PloS one · 2015Article
- PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.Bioinformatics (Oxford, England) · 2014Article
- A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration.BMC bioinformatics · 2013Article
- Peppy: proteogenomic search software.Journal of proteome research · 2013Article
- The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis.Cell host & microbe · 2013Article
- Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundHigh-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.
resultsThe Proteogenomic Mapping Tool includes a Java implementation of the Aho-Corasick string searching algorithm which takes as input standardized file types and rapidly searches experimentally observed peptides against a given genome translated in all 6 reading frames for exact matches. The Java implementation allows the application to scale well with larger eukaryotic genomes while providing cross-platform functionality.
conclusionsThe Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data.
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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.