Abacus 20160720 – Extracting Spectral Counts from MS/MS Data Sets.

Abacus 20160720

:: DESCRIPTION

Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOs
  • Java

:: DOWNLOAD

Abacus 

:: MORE INFORMATION

Citation:

Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650. Epub 2011 Feb 17.
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.

Luciphor2 – PTM-site localization on MS/MS data

Luciphor2

:: DESCRIPTION

Luciphor2 is a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Luciphor2

:: MORE INFORMATION

Citation:

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
Fermin D, Avtonomov D, Choi H, Nesvizhskii AI

TPP 5.2 – Collection of integrated tools for MS/MS Proteomics

TPP 5.2

:: DESCRIPTION

TPP (Trans-Proteomic Pipeline) is a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.

::DEVELOPER

Seattle Proteome Center

:: SCREENSHOTS

TPP

:: REQUIREMENTS

  • Windows / Mac OsX / Linux

:: DOWNLOAD

  TPP 

:: MORE INFORMATION

Citation

Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.
Trans-proteomic pipeline: a pipeline for proteomic analysis.
Pedrioli PG.

OMSSA 2.1.9 / COMPASS 1.4.1 – MS/MS Peptide Spectra Identification

OMSSA 2.1.9 / COMPASS 1.4.1

:: DESCRIPTION

OMSSA [ Open Mass Spectrometry Search Algorithm] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST.

COMPASS is the Coon OMSSA (Open Mass Spectrometry Search Algorithm) Proteomic Analysis Software Suite.

::DEVELOPER

National Center for Biotechnology Information / The Coon Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

 OMSSA  / COMPASS

:: MORE INFORMATION

Citation:

Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ.
COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA,
Proteomics, 2011; 11(6): 1064–74

J Proteome Res. 2004 Sep-Oct;3(5):958-64.
Open mass spectrometry search algorithm.
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH.

FragmentationAnalyzer 1.5.13 – Analyze MS/MS Fragmentation Data

FragmentationAnalyzer 1.5.13

:: DESCRIPTION

Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data.

::DEVELOPER

Harald Barsnes

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 FragmentationAnalyzer

:: MORE INFORMATION

Citation

Proteomics. 2010 Mar;10(5):1087-90.
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.
Barsnes H, Eidhammer I, Martens L.

MascotDatfile 3.4.31 – java API for MS/MS search results by Mascot

MascotDatfile 3.4.31

:: DESCRIPTION

 MascotDatfile is an open-source library to fully parse and analyse MASCOT MS/MS search results.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MascotDatfile

:: MORE INFORMATION

Citation

Helsens et al.
MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.
Proteomics (2007) vol. 7 (3) pp. 364-6

Peptizer 1.8.4 – Automating manual Validation of MS/MS Search results

Peptizer 1.8.4

:: DESCRIPTION

The Peptizer platform was created to automate the manual validation process by an expert system. The user can create a rule set via by enabling a set of Agent objects that will each inspect an assumption based on expert knowledge. Subsequent aggregation of multiple Agent inspection the enables separation of peptide identifications by these rules.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Peptizer

:: MORE INFORMATION

Citation

Helsens et al.
Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results.
Molecular & cellular proteomics : MCP (2008) vol. 7 (12) pp. 2363-72.

X!TandemPipeline 3.3.4 – Peptide / Protein Identifications from MS/MS Mass Spectra

X!TandemPipeline 3.3.4

:: DESCRIPTION

X!TandemPipeline is a free software that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

::DEVELOPER

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

:: SCREENSHOTS

XTandemPipeline

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

  X!TandemPipeline

:: MORE INFORMATION

SimLipid 4.40 – Characterize lipids using Data from MS, MS/MS and MSE

SimLipid 4.40

:: DESCRIPTION

SimLipid is a comprehensive informatics tool for characterizing lipids using precursors and product ions data from MS, MS/MS and MSE data.

Lipidomics is an emerging field of systems biology being applied to disease research, drug discovery and biomarker identification. Mass spectrometry is one of the most sophisticated technologies for identification and quantification of lipids from biological mixtures. However, the major challenge in mass spectrometric data analysis is the huge amount of data generated in the process. Some of the most important aspects of mass spectrometric lipidome data analysis are the high throughput quantitative analysis of crude lipid extracts and structural identification of lipids using precursor and product ion data.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimLipid DemoGet a free Key

:: MORE INFORMATION

Order SimLipid

SimGlycan 5.40 – Glycan & Glycopeptide MS/MS Data Analysis Tool

SimGlycan 5.40

:: DESCRIPTION

SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragments and generates a list of probable candidate structures.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimGlycan DemoGet a free Key

:: MORE INFORMATION

Order SimGlycan