The proteogenomic mapping tool

William S. Sanders, Nan Wang, Susan M. Bridges, Brandon M. Malone, Yoginder S. Dandass, Fiona M McCarthy, Bindu Nanduri, Mark L. Lawrence, Shane C Burgess

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number115
JournalBMC Bioinformatics
Volume12
DOIs
StatePublished - Apr 22 2011
Externally publishedYes

Fingerprint

Genome
Genes
Peptides
Proteomics
Mass Spectrometry
Java
Mass spectrometry
Annotation
String searching algorithms
Genetic Code
Reading Frames
Peptide Mapping
Proteogenomics
Computer operating systems
Research
Operating Systems
Personal computers
Computer hardware
High Throughput
High Speed

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Sanders, W. S., Wang, N., Bridges, S. M., Malone, B. M., Dandass, Y. S., McCarthy, F. M., ... Burgess, S. C. (2011). The proteogenomic mapping tool. BMC Bioinformatics, 12, [115]. https://doi.org/10.1186/1471-2105-12-115

The proteogenomic mapping tool. / Sanders, William S.; Wang, Nan; Bridges, Susan M.; Malone, Brandon M.; Dandass, Yoginder S.; McCarthy, Fiona M; Nanduri, Bindu; Lawrence, Mark L.; Burgess, Shane C.

In: BMC Bioinformatics, Vol. 12, 115, 22.04.2011.

Research output: Contribution to journalArticle

Sanders, WS, Wang, N, Bridges, SM, Malone, BM, Dandass, YS, McCarthy, FM, Nanduri, B, Lawrence, ML & Burgess, SC 2011, 'The proteogenomic mapping tool', BMC Bioinformatics, vol. 12, 115. https://doi.org/10.1186/1471-2105-12-115
Sanders WS, Wang N, Bridges SM, Malone BM, Dandass YS, McCarthy FM et al. The proteogenomic mapping tool. BMC Bioinformatics. 2011 Apr 22;12. 115. https://doi.org/10.1186/1471-2105-12-115
Sanders, William S. ; Wang, Nan ; Bridges, Susan M. ; Malone, Brandon M. ; Dandass, Yoginder S. ; McCarthy, Fiona M ; Nanduri, Bindu ; Lawrence, Mark L. ; Burgess, Shane C. / The proteogenomic mapping tool. In: BMC Bioinformatics. 2011 ; Vol. 12.
@article{1b8e7ed917a242989924e2436a61b1df,
title = "The proteogenomic mapping tool",
abstract = "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.",
author = "Sanders, {William S.} and Nan Wang and Bridges, {Susan M.} and Malone, {Brandon M.} and Dandass, {Yoginder S.} and McCarthy, {Fiona M} and Bindu Nanduri and Lawrence, {Mark L.} and Burgess, {Shane C}",
year = "2011",
month = "4",
day = "22",
doi = "10.1186/1471-2105-12-115",
language = "English (US)",
volume = "12",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",

}

TY - JOUR

T1 - The proteogenomic mapping tool

AU - Sanders, William S.

AU - Wang, Nan

AU - Bridges, Susan M.

AU - Malone, Brandon M.

AU - Dandass, Yoginder S.

AU - McCarthy, Fiona M

AU - Nanduri, Bindu

AU - Lawrence, Mark L.

AU - Burgess, Shane C

PY - 2011/4/22

Y1 - 2011/4/22

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=79955002352&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79955002352&partnerID=8YFLogxK

U2 - 10.1186/1471-2105-12-115

DO - 10.1186/1471-2105-12-115

M3 - Article

C2 - 21513508

AN - SCOPUS:79955002352

VL - 12

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

M1 - 115

ER -