MR-MSPOLYGRAPH / MSPolygraph 1.61 – MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-scale Peptide Identification

MR-MSPOLYGRAPH / MSPolygraph 1.61

:: DESCRIPTION

MR-MSPOLYGRAPH is a MapReduce based implementation for parallelizing peptide identification from mass spectrometry data

MSPolygraph is an open source hybrid database and spectral library MS/MS search engine that runs in either serial or parallel modes. MSPolygraph examines the ions in MS/MS spectra to identify likely matching candidate peptides from a reference database of protein sequences (.Fasta file). MSPolygraph also supports searching a spectral library (collection of annotated MS/MS spectra).

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MR-MSPOLYGRAPH / MSPolygraph

:: MORE INFORMATION

Citation

A. Kalyanaraman, W.R. Cannon, B. Latt, D.J. Baxter (2011).
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.
Bioinformatics (2011) 27 (21): 3072-3073. doi: 10.1093/bioinformatics/btr523.

Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, A. Heredia-Langner, G.A. Anderson, and K.J. Auberry. 2005.
Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data”,
J. Proteome Research, 4(5): 1687-169

Tremolo 20130821 – Spectral Library Search

Tremolo 20130821

:: DESCRIPTION

Tremolo is a spectral library search tool that leverages the Spectral Library Generating Function (SLGF) concept to identify spectrum-spectrum matches (SSMs).

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Tremolo

:: MORE INFORMATION

Citation

J Proteome Res. 2013 Sep 6;12(9):3944-51. doi: 10.1021/pr400230p. Epub 2013 Jul 31.
Spectral library generating function for assessing spectrum-spectrum match significance.
Wang M1, Bandeira N.

MSPLIT 1.0 – Multiplexed Spectral Library Search

MSPLIT 1.0

:: DESCRIPTION

M-SPLIT is a spectral-library search tool for identification of mixture spectra of up to two peptides.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MSPLIT

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2010 Jul;9(7):1476-85. doi: 10.1074/mcp.M000136-MCP201. Epub 2010 Mar 27.
Peptide identification from mixture tandem mass spectra.
Wang J1, Pérez-Santiago J, Katz JE, Mallick P, Bandeira N.