Category: proteomics

ms-lims 7.7.7 – Mass Spectrometry based Proteomics Information Management System

ms-lims 7.7.7

:: DESCRIPTION

The ms_lims project provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 ms-lims

:: MORE INFORMATION

Citation

Proteomics. 2010 Mar;10(6):1261-4.
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.
Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L.

Peppy – Proteogenomic, Proteomic search tool

Peppy

:: DESCRIPTION

Peppy: a fully integrated, proteogenomic mapping software tool. Peppy generates a peptide database from genome files, tracks peptide loci, matches peptides to MS/MS spectra, assigns scores to those matches, and tracks score distributions to find E-Values. To determine false discovery rate thresholds, Peppy automatically generates a decoy database from the original genome files and repeats the entire search process.

::DEVELOPER

The Giddings Lab at Boise State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Peppy

:: MORE INFORMATION

Citation

Peppy: proteogenomic search software.
Risk BA, Spitzer WJ, Giddings MC.
J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w.

mMass 5.5.0 – Open Source Mass Spectrometry Tool

mMass 5.5.0

:: DESCRIPTION

mmass is a software by a mass spectrometrist that is an excellent mass spectrum viewer with other features related to proteomics;

::DEVELOPER

Martin Strohalm, PhD.

:: SCREENSHOTS

mMass

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

 mMass

:: MORE INFORMATION

Citation:

mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra
Niedermeyer THJ and Strohalm M
PLoS ONE 7 (9), e44913 (2012)

InSilicoSpectro 1.3.24 – Open-source Proteomics Library

InSilicoSpectro 1.3.24

:: DESCRIPTION

InSilicoSpectro is a proteomics open-source project,aimed at implementing recurrent computations that are necessary for proteomics data analysis.

::DEVELOPER

Alexandre Masselot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 InSilicoSpectro

:: MORE INFORMATION

Citation

J Proteome Res. 2006 Mar;5(3):619-24.
InSilicoSpectro: an open-source proteomics library.
Colinge J, Masselot A, Carbonell P, Appel RD.

MUMAL – Multivariate Analysis in Shotgun Proteomics

MUMAL

:: DESCRIPTION

MUMAL is a new method, termed for PSM assessment that is based on machine learning techniques. The method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives.

:: DEVELOPER

Fabio R. Cerqueira  (fabio.cerqueira@ufv.br); Ricardo S. Ferreira; Alcione P. Oliveira; Humberto J. O. Ramo; Christian Baumgartner.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 MUMAL

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 5:S4. doi: 10.1186/1471-2164-13-S5-S4. Epub 2012 Oct 19.
MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.
Cerqueira FR, Ferreira RS, Oliveira AP, Gomes AP, Ramos HJ, Graber A, Baumgartner C.

MUDE 1.0 – Assess MS/MS Spectra Assignments

MUDE 1.0

:: DESCRIPTION

mude (multivariate decoy database analysis) is a set of programs implementing the framework to assess MS/MS spectra assignments

:: DEVELOPER

By Cerqueira, Fabio (fabio.cerqueira@ufv.br); Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 MUDE

:: MORE INFORMATION

Citation

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.
Cerqueira FR, Graber A, Schwikowski B, Baumgartner C.
J Proteome Res. 2010 May 7;9(5):2265-77. doi: 10.1021/pr901023v.

PWIMS 2.3 – Proteomics Workflow and Information Management System

PWIMS 2.3

:: DESCRIPTION

PWIMS is an information management system designed as client-server tool for handling Proteomics Experiments. It has features for 2DGe image capturing, Protocol Management, Mass spec data integration, sample management etc.

::DEVELOPER

Bioinformatics Group, Roskamp Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • LAMPP (Linux-Apache-MySQL-Perl/PHP) environment

:: DOWNLOAD

 PWIMS

:: MORE INFORMATION

Citation

Venkatarajan Mathura, Deepak Kolippakkam, Sarah Wilson, Freya Geall, Hong Wang, Fiona Crawford, Michael Mullan., 2004
“PWIMS 1.0: Proteomics Workflow and Information Management System”,
Society of Neuroscience, 34th Annual Meeting.

MapQuant 2.1.1 – Large-scale Protein Quantification

MapQuant 2.1.1

:: DESCRIPTION

MapQuant is a program that given large mass-spectrometry data, outputs quantitation for any organic species in the sample. The quantification involves several algorithms that are applied to the data after they are formatted into a data-structure called a two-dimensional map.

::DEVELOPER

George M. Church Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Perl

:: DOWNLOAD

 MapQuant

:: MORE INFORMATION

Citation

Leptos, KC, Sarracino, DA, Jaffe, JD, Krastins B, Church, GM (2006)
MapQuant: Open-Source Software for Large-Scale Protein Quantitation,
Proteomics. 2006 Mar;6(6):1770-82.

PepDistiller 1.26 – Improve Sensitivity & Accuracy of Peptide Identifications in Shotgun Proteomics

PepDistiller 1.26

:: DESCRIPTION

PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.

::DEVELOPER

Beijing Proteome Research Center Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • ActivePerl

:: DOWNLOAD

 PepDistiller

:: MORE INFORMATION

Citation

Proteomics. 2012 Jun;12(11):1720-5. doi: 10.1002/pmic.201100167.
PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics.
Li N, Wu S, Zhang C, Chang C, Zhang J, Ma J, Li L, Qian X, Xu P, Zhu Y, He F.