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Project status key: |
U = Unknown
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A = Alpha
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B = Beta
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R = Release
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Organisation |
Product |
Version (date) |
Contact person |
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R
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Bruker Daltonics / Protagen |
ProteinScape (registered users navigate to 'Service & Support', 'Software Support / Downloads') |
1.3 (2005-12-01) |
Herbert Thiele |
| ProteinScape™ is able to manage the whole proteomics process from sample collection, protein separation, spot picking, protein digestion, sample preparation, mass spectrometry, and database search for protein identification. |
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R
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Bruker Daltonics |
CompassXport (registered users navigate to 'Service & Support', 'Software Support / Downloads') |
1.3 (?) |
Herbert Thiele |
| CompassXport 1.3 is a free software tool for the extraction of essential MS and MS/MS(n) data from Bruker ESI and MALDI acquisition files. As an exciting new feature version 1.3 now allows the export to mzData 1.05 format. |
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R
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GeneBio |
Phenyx |
2.0 (na) |
phenyx@genebio.com |
| Software platform for the identification and characterization of proteins and peptides from mass spectrometry data |
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R
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Indigo BioSystems |
Rubicon |
2.1 (2008-03) |
Randy Julian |
| The Rubicon suite of applications from Indigo BioSystems includes GLP quality mzData converters and data analysis tools, including mass spectrometry and chromatography data visualization. The Rubicon Repository uses mzData and other HUPO-PSI standards to enable scientific collaboration and data interchange as well as long term storage. |
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R
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Institute of Chemical Technology in Prague - Department of Biochemistry and Microbiology |
mMass |
2.1 beta 4
(2006-07-31) |
Contact page |
| Program mMass presents an open source package of simple tools for mass spectrometric data analysis. It consist of several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks. As the program is written in Python language, uses wxPython libraries for graphic user interface and is released under GNU General Public License, it is portable to many computer platforms and has a good potential to be easily modified or extended by modules of specific need. |
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R
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ProteomeCommons.org |
ProteomeCommons.org DFS |
248 (2006-05-08) |
Jayson Falkner |
| A free to use, open-source system for sharing raw proteomics data and linking it to annotations. This system is coded in Java and implemented as a secured peer to peer network for hosting virtually unlimited users and unlimited amounts of data. It is particularly well suited for manuscript style publications, including support for password-protecting data during the peer review process. When downloading data users may opt to auto-convert the data in to a variety of different formats including mzData. |
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R
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ProteomeCommons.org |
ProteomeCommons.org IO Framework |
4.4 (2006-05-01) |
Jayson Falkner |
| This is a free, open-source, Java framework for handling spectra and peak list files. The framework can read and write to a number of different spectra and peak list formats, and the framework provides a simple, intuitive Java object model for working with spectra or peak lists. The overall goal of this project is to make working with peak list or spectral data easy, even if you are working with various different file formats or if you are working with incredibly large files. Additionally, we aren't trying to lock developers in to using Java. Utility programs are included that will translate peak list or spectral data in to a simple, plain text format that is well-suited for pasing via regular expressions in perl, python, vbscript, or any other programming language. |
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R
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Seattle Proteome Center |
Trans-Proteomic Pipeline |
2.8.2
(2006-04-06) |
info@proteomecenter.org |
| The TPP includes all steps of the ISB MS/MS analysis pipeline after results of database search: Peptide validation, Peptide quantitation, Protein identification, and Protein quantitation. XML-based, the TPP is easily extensible to additional search engines and analysis modules. |
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A
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Swegene Bioinformatics Facility, Lund |
Proteios |
2.x (2006-05-05) |
Mailing lists |
| Proteios is a comprehensive database server to manage the massive amounts of data generated by proteomics experiment and analysis. In short, it manages and tracks biomaterial information, raw data and images, and provides integrated and plugin-able data viewing and analysis tools. The organization and interface of Proteios is designed to closely follow the natural work-flow of the proteomics researchers. |
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R
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Swiss Institute of Bioinformatics,
Proteome Informatics Group |
Aldente |
2005-10-12 |
Christine Hoogland |
Aldente is a tool to identify proteins from peptide mass fingerprinting data.
This new, fast and powerful tool takes advantage of the Hough transform for spectra recalibration and outlier exclusion. |
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B
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Swiss Institute of Bioinformatics,
Proteome Informatics Group |
Popitam |
na (na) |
Patricia Hernandez |
| "Open-modification search" — MS/MS identification method to identify and characterize peptides with mutations or unexpected post-translational modifications. |
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R
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The GPM Organization |
X! P3 |
2006.05.01 |
contact@thegpm.org |
| An open source tandem mass spectrum search engine that uses proteotypic peptide information to assist in the assignment of peptide sequences to experimental mass spectra. |
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R
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Thermo Electron Corporation |
Bioworks |
3.2 EF1 (na) |
Contact (support) link |
| BioWorks is a software suite for identification and characterization of peptides and proteins featuring the SEQUEST search algorithm. mzData import and export functions are included as part of BioWorks 3.2 EF1. |
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R
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Waters Corporation |
ProteinLynx Global Server |
2.2.5 (2006-05) |
Ronan O'Malley |
| Waters ProteinLynx Global SERVER 2.2.5 is Waters’ fully integrated, scalable proteomics platform, featuring a comprehensive range of leading data processing and interpretation tools for qualitative and quantitative proteomics. |
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