Software for 2D PAGE & MS
From MyBio
Contents |
[edit] Categories which link here
[edit] Software for 2D PAGE
For a detailled description of the analysis workflow please review the open source article The state of the art in the analysis of two-dimensional gel electrophoresis images.
Particularly the different approaches regarding spot matching help to distinguish between the software packages and their demand for manual interaction.
[edit] Open Source
Open Source systems have been developed by academic groups.
Flicker (time stamp: 2007/12/04)
Flicker is an open source Java application for comparing 2D gel (or similar) images across the Internet or locally. It is possible to visually compare a user gel image with a SWISS-2DPAGE image and then select spots for identification with the Expasy SWISS-PROT protein ID database. It also has rudimentary manual quantification of spot data.
Open2Dprot (time stamp: 2006/03/20)
Open2Dprot n-dimensional proteomics exploratory data analysis software. It is an open source Java project Open2Dprot for proteomics exploratory data analysis. It was derived from the old UNIX GELLAB-II, new Java Flicker 2D gel image comparison, and Java MAExplorer DNA microarray data mining projects.
JVirGel (time stamp: 2006)
Calculation of virtual two-dimensional protein gels. creates and visualizes virtual 2D protein gels based on migration behaviour of proteins in dependence of their theoretical molecular weights in combination with their isoelectric points (calc). The utilization of all proteins of an organism of interest deduced from genes of the corresponding genome project in combination with the elimination of obvious membrane proteins permits the creation of an optimized calculated proteome map. The electrophoretic separation behaviour of single proteins is accessible interactively in a Java applet by selecting a pI/MW range and an electrophoretic timescale of interest. The calculated pattern of protein spots helps to identify unknown proteins and to localize known proteins during experimental proteomics approaches. Differences between the experimentally observed and the calculated migration behaviour of certain proteins provide first indications for potential protein modification events. When possible, protein spots are linked via mouse-clicks to SWISS-PROT and PRODORIC.
GELLAB-II 2D (time stamp: 2004/08/08)
GELLAB-II 2D gel exploratory data analysis software. GELLAB-II was an integrated collection of programs for the analysis of 2D electrophoretic gels. It ran only on UNIX systems. These programs were developed at the Image Processing Section in the NCI Laboratory of Computational and Experimental Biology. A more recent open source Java project Open2Dprot for n-dimensional proteomics exploratory data analysis was derived from GELLAB-II, new Flicker 2D gel image comparison, and MAExplorer DNA microarray data mining projects.
TopSpot (time stamp: 2004)
Scanning the gel, editing the spots and saving the information.
CAROL (project completed: 2000/12/31)
2D Gel Matching.
[edit] Commercial packages based on image warping
[edit] Bio-Rad
PDQuest 2-D Analysis Software
PDQuest offers best-in-class performance for analysis and databasing of 2-D gels. PDQuest software offers powerful comparative analysis and is specifically designed for laboratories that analyze many gels at once.
[edit] DECODON
Delta2D Advanced image processing software for 2D gel analysis
This is a complete software package for analysing of whole sets of 2-D electrophoresis gels and uses advanced image processing technology to compensate for the variations in spot positions from one gel to another.
[edit] Nonlinear Dynamics
Phoretix links
Home. Contact Us. About Us. Products. Coverwise Support. Training Services. News & Events. Careers. Download Centre. Latest News 8th August 2006 BioMachines Inc adopt Nonlinear Dynamics' SameSpots approach for 2D image analysis Read More ...
[edit] Commercial packages based on spot pattern matching
[edit] GE Healthcare
DeCyder Differential Analysis Software
DeCyder™ v6.5 Differential Analysis Software has been specifically developed as a key element of the Ettan™ DIGE system. This proprietary software significantly increases throughput by accurately addressing measurement of protein differences with statistical confidence and reducing hands-on time from days to minutes with minimal user-to-user variation.
[edit] Genebio
ImageMaster 2D Platinum & Melanie Viewer
This software is completely based on the well-known Melanie analysis package and is distributed by GE Healthcare.Software is used for analysing, annotating and querying complex 2-D gel samples.
[edit] Software for 2D PAGE Web-Databases
Make2DDB
Package preparing the data and the programs necessary to bu.
Proteome 2D-PAGE Database - Software Tools
Proteome 2D-PAGE Database - Software Tools Program Description Download TopSpot © Scanning the gel, editing the spots and saving the information TopSpot.zip. Fragmentation © Fragmentation of the gel image into sections Fragmentation.zip. ...
[edit] MS - Software and Web Resources
SpectralWorks Ltd.
Vendor-independent software applications for data analysis of MS data. Includes biological applications using GC and LC separations, registration form and contacts in Runcorn, England.
Amdis Home
Automated mass spectral deconvolution and identification system software for interpretation, including chemometrics, GC and LC-MS data and mass spectrometry interpretation, from NIST, Boulder, Colorado.
RIZA GCMS Database
"This is a tool for archiving, searching and quantitating previously acquired GCMS data.The RIZA GCMS database saves the 20 'most important' mass peaks for each MS-spectrum along with its Kovats (retention) index.
SpecAlign
Designed for pre-processing of SELDI and alignment of each spectrum, for clinical proteomic data and analysis of other spectral or chromatographic types. Includes documentation, FAQ, forum, downloads from the Cartwright Group, at University of Oxford, Eng
ACD/MS Manager - Advanced Chemistry Department
It is a software designed to conveniently process, interpret MS data, and easily communicate results. In its entry-level configuration, it can process mass spectra (MS), tandem mass spectra (MS/MS, MS/MS/MS, MSn) or hyphenated data sets.
MassFinder
Details of program for interpretation, identification and administration of GC/MS data, including terpenoids library for essential oils analysis, and GC/MS-SIM quantification. Also offers customized development from Hochmuth Scientific Consulting, Berlin.
BET2 Software
Products for the identification of structures for isomers with similar mass spectra, by differential mass spectrometry.
Wsearch Software
Supports viewing of native mass spectrometry data, in a number of file formats and two mass spectral library formats. Features FTIR and X-Ray, with contacts in Melbourne, Victoria.
General Protein Mass Analysis for Windows
The main design goals of the program have been ease-of-use without sacrificing speed and precision.
Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB)
This software was specifically developed for the representation of mass spectra along with data from the separation step,allows graphical exploration inside huge datasets and gives the scientist access to information that previously was hidden.
Phenyx-a software platform for MS
A software platform for the identification and characterization of proteins and peptides from mass spectrometry data.
