ProteinDecision 1.0 – Protein Identification using Peptide-Mass Fingerprinting Data

ProteinDecision 1.0

:: DESCRIPTION

ProteinDecision is a computer software for identifying protein by serching against protein database with the input Peptide-Mass Fingerprinting Data. It can handle the issues of selecting peaks from mass spectrum, transforming database format, displaying the top ranks of identification result, and detailed information for each ranking.

::DEVELOPER

Digital Biology Laboratory, University Of Missouri-Columbia

:: SCREENSHOTS

ProteinDecision

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 ProteinDecision

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:7-22. doi: 10.1007/978-1-60761-444-9_2.
Bioinformatics methods for protein identification using Peptide mass fingerprinting.
Song Z1, Chen L, Xu D.

MsPI 1.2 – Tool for Protein Identification by PMF

MsPI 1.2

:: DESCRIPTION

MsPI is a Perl procedure for protein identification by PMF. The implemented scoring methods were derived from the literature. MsPI implements a strategy to remove the contaminant masses present in the acquired spectra.

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Perl

:: DOWNLOAD

  MsPI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S11.
A Perl procedure for protein identification by Peptide Mass Fingerprinting.
Tiengo A, Barbarini N, Troiani S, Rusconi L, Magni P.

Mayu 1.08 – Protein Identification False Discovery Rates

Mayu 1.08

:: DESCRIPTION

Mayu is a software package for the analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 Mayu

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2009 Nov;8(11):2405-17. doi: 10.1074/mcp.M900317-MCP200. Epub 2009 Jul 16.
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry.
Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R.

DeNovo Pipeline 1.5 – Protein Identification by de novo Interpretation

DeNovo Pipeline 1.5

:: DESCRIPTION

DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

denovo_pipeline

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 DeNovo Pipeline

:: MORE INFORMATION

MetaPepSeq 0.8 Beta – Protein Identification in Mass Spectrometry Experiments.

MetaPepSeq 0.8 Beta

:: DESCRIPTION

MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 MetaPepSeq

:: MORE INFORMATION