Tag: Proteomics

PIQMIe 1.0 – Proteomics Identifications & Quantitations Data Management & Integration Service

PIQMIe 1.0

:: DESCRIPTION

PIQMIe is a web-based tool that aids in the data management, analysis and visualization of semi-quantitative mass spectrometry (MS)-based proteomics experiments, in particular those using the stable isotope labeling with amino acids in cell culture (SILAC).

::DEVELOPER

PIQMIe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PIQMIe

:: MORE INFORMATION

Citation

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.
Kuzniar A, Kanaar R.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W100-6. doi: 10.1093/nar/gku478.

ProteoWizard 3.0.21193 – Proteomics Data Analysis

ProteoWizard 3.0.21193

:: DESCRIPTION

ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis.The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

::DEVELOPER

ProteoWizard Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

ProteoWizard

:: MORE INFORMATION

Citation

Kessner D, Chambers M, Burke R, Agus D, Mallick P.
ProteoWizard: open source software for rapid proteomics tools development.
Bioinformatics. 2008 Nov 1;24(21):2534-6. Epub 2008 Jul 7.

MSnbase 2.19.1 – Base Functions and Classes for MS-based Proteomics

MSnbase 2.19.1

:: DESCRIPTION

MSnbase is an R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. It provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation.

::DEVELOPER

Dr Laurent Gatto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 MSnbase

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 15;28(2):288-9. doi: 10.1093/bioinformatics/btr645. Epub 2011 Nov 22.
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.
Gatto L, Lilley KS.

MSAcquisitionSimulator 1.0.2 – Data-dependent Acquisition Simulator for LC-MS Shotgun Proteomics

MSAcquisitionSimulator 1.0.2

:: DESCRIPTION

MSAcquisitionSimulator is a collection of three command-line tools that simulate data-dependent acquisition algorithms on in silico generated ground truth data of liquid chromatography-mass spectrometry proteomics experiments.

::DEVELOPER

Major Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MSAcquisitionSimulator

:: MORE INFORMATION

Citation

MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics.
Goldfarb D, Wang W, Major MB.
Bioinformatics. 2015 Dec 17. pii: btv745.

Perseus v1.6.15.0 – Shotgun Proteomics Data Analysis

Perseus v1.6.15.0

:: DESCRIPTION

Perseus is a software package for shotgun proteomics data analysis, which helps researchers to extract biologically meaningful information from their MaxQuant output such as posttranslational modifications.

::DEVELOPER

Jürgen Cox

:: SCREENSHOTS

Perseus

:: REQUIREMENTS

  • Windows 64bit
  • .NET Framework 4.5

:: DOWNLOAD

 Perseus

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 16:S12. doi: 10.1186/1471-2105-13-S16-S12. Epub 2012 Nov 5.
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.
Cox J, Mann M.

ProCon 0.9.804 – PROteomics CONversion tool

ProCon 0.9.804

:: DESCRIPTION

ProCon is a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 ProCon

:: MORE INFORMATION

Citation

ProCon – PROteomics CONversion tool.
Mayer G, Stephan C, Meyer HE, Kohl M, Marcus K, Eisenacher M.
J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015.

PeakQuant 1.5.47 – Proteomics Software Suit

PeakQuant 1.5.47

:: DESCRIPTION

PeakQuant (formerly known as Peakardt) serves as an integrated platform for several Proteomics tools and provides an easily operated graphical user interface.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 PeakQuant

:: MORE INFORMATION

Citation

OMICS. 2012 Sep;16(9):457-67. doi: 10.1089/omi.2011.0140. Epub 2012 Aug 21.
Find pairs: the module for protein quantification of the PeakQuant software suite.
Eisenacher M1, Kohl M, Wiese S, Hebeler R, Meyer HE, Warscheid B, Stephan C.

Mass-Up 1.0.14 – Mass Spectrometry Utility for Proteomics

Mass-Up 1.0.14

:: DESCRIPTION

Mass-Up is an open-source mass spectrometry software for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data.

::DEVELOPER

The SING research group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Mass-Up

:: MORE INFORMATION

Citation:

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery.
López-Fernández H, Santos HM, Capelo JL, Fdez-Riverola F, Glez-Peña D, Reboiro-Jato M.
BMC Bioinformatics. 2015 Oct 5;16(1):318. doi: 10.1186/s12859-015-0752-4.

ProteomeScout – Visualization and Analysis Framework for Proteins

ProteomeScout

:: DESCRIPTION

ProteomeScout is a database of proteins and post-translational modifications.

::DEVELOPER

The Naegle Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Web Server
  • MySQL

:: DOWNLOAD

ProteomeScout

:: MORE INFORMATION

Citation:

Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.
ProteomeScout: A web resource for analysis of high-throughput post-translational proteomic studies.
Molecular and Cellular Proteomics, 2010.

Mol Cell Proteomics. 2010 Nov;9(11):2558-70. doi: 10.1074/mcp.M110.001206.
PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.
Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.

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