BACKGROUND: High-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. RESULTS: The 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. CONCLUSIONS: The 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.
BACKGROUND: High-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. RESULTS: The 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. CONCLUSIONS: The 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.
Authors: Fiona M McCarthy; Amanda M Cooksey; Nan Wang; Susan M Bridges; G Todd Pharr; Shane C Burgess Journal: Proteomics Date: 2006-05 Impact factor: 3.984
Authors: Joel R Sevinsky; Benjamin J Cargile; Maureen K Bunger; Fanyu Meng; Nathan A Yates; Ronald C Hendrickson; James L Stephenson Journal: J Proteome Res Date: 2007-12-07 Impact factor: 4.466
Authors: Natalie E Castellana; Samuel H Payne; Zhouxin Shen; Mario Stanke; Vineet Bafna; Steven P Briggs Journal: Proc Natl Acad Sci U S A Date: 2008-12-19 Impact factor: 11.205
Authors: Kelly V Ruggles; Karsten Krug; Xiaojing Wang; Karl R Clauser; Jing Wang; Samuel H Payne; David Fenyö; Bing Zhang; D R Mani Journal: Mol Cell Proteomics Date: 2017-04-29 Impact factor: 5.911
Authors: Christoph N Schlaffner; Georg J Pirklbauer; Andreas Bender; Judith A J Steen; Jyoti S Choudhary Journal: J Vis Exp Date: 2018-05-22 Impact factor: 1.355
Authors: Olga T Schubert; Jeppe Mouritsen; Christina Ludwig; Hannes L Röst; George Rosenberger; Patrick K Arthur; Manfred Claassen; David S Campbell; Zhi Sun; Terry Farrah; Martin Gengenbacher; Alessio Maiolica; Stefan H E Kaufmann; Robert L Moritz; Ruedi Aebersold Journal: Cell Host Microbe Date: 2013-05-15 Impact factor: 21.023
Authors: Adly M M Abd-Alla; Henry M Kariithi; François Cousserans; Nicolas J Parker; İkbal Agah İnce; Erin D Scully; Sjef Boeren; Scott M Geib; Solomon Mekonnen; Just M Vlak; Andrew G Parker; Marc J B Vreysen; Max Bergoin Journal: J Gen Virol Date: 2016-01-21 Impact factor: 3.891
Authors: Gloria M Sheynkman; Michael R Shortreed; Anthony J Cesnik; Lloyd M Smith Journal: Annu Rev Anal Chem (Palo Alto Calif) Date: 2016-03-30 Impact factor: 10.745