TPP:Related Tools
From SPCTools
Contents |
Introduction
The TPP has many relationships with other software programs and projects. Some of these, like the TPP itself, are freely-available open-source projects, while others are commercial. Some of these tools provide compatible data formats that can be used as input to the TPP, while others repackage or redistribute the TPP itself, or work with the data produced by the TPP.
Compatible Mass-Spectrometer Instrument-Specific Software and File Formats
Thermo (Xcalibur) .RAW files
Waters (MassLynx) .RAW directories
MDS/Sciex (Analyst) .wiff files
Agilent (MassHunter) .d directories
The TPP aims to support a wide variety of mass-spec instrument formats; the TPP provides tools to convert their proprietary formats into our open mzXML format. Please see Formats:mzXML for an overview of compatible formats and converter software.
| Vendor | Instrument Acquisition Software | File Type | TPP mzXML converter |
|---|---|---|---|
| Thermo | XCalibur | .RAW file | ReAdW |
| Waters | MassLynx | .RAW directory | wolf |
| MDS/Sciex for ABI and Agilent | Analyst, AnalystQS | .wiff file | mzWiff (beta, not yet released) |
| Agilent | MassHunter | .d directory | trapper (beta, not yet released) |
Compatible Mass-Spectroscopy Input File Formats
mzXML
mzData
mzML
In addition to the SPC-developed open MS format mzXML, the TPP can also read the HUPO Proteome Standards Initiative (PSI) mzData format. Support is ongoing for the next-generation format called mzML, developed through collaboration between PSI, instrument vendors, the SPC, and other proteomics software companies.
Compatible Sequence Search Engines
All of the programs attempt to assign an amino acid peptide identification to a MS2 spectra. The TPP includes tools to convert the proprietary search engine output file into the TPP's native, open format called pepXML. We always welcome opportunities to add support for additional search engines. For information about working with these search engines please see TPP:Supported Search Engines
Compatible search engines, added in order of support:
SEQUEST
SEQUEST is a commercial search engine, currently sold by Thermo.
ProbID
ProbIDis an open-source, freely-available SPC developed search engine.
Mascot
Mascot is a commercial search engine, distributed by Matrix Science.
X!Tandem
X!Tandem is a open-source, free search engine. X!Tandem with the K-Score plugin is now distributed as part of the Windows TPP (as of version 3.2.1).
Phenyx
Phenyx is a commercial search engine.
Other tools and projects
SBEAMS
SBEAMS is a high-powered, free and open-source SPC-developed LIMS system. The SBEAMS proteomics module was designed for TPP data. SBEAMS is the backend for PeptideAtlas (see below).
PeptideAtlas
PeptideAtlas: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB.
The Gaggle
The Gaggle project: The ISB's open-source data interaction, visualization, and exploration system, increasingly integrated with the TPP.
Cytoscape
Cytoscape Project: Open-source network visualization tool, integrated with the Gaggle, co-developed at the ISB.
IPP (InSilicos)
InSilicos produces the InSilicos Proteomics Pipeline, or IPP; this is a native-windows build of the TPP code which is claimed to be faster than the TPP's Windows distribution. InSilicos provides consultant-based support services for the IPP. InSilicos has contributed important code to the TPP's code base and plays a role in TPP support.
CPAS (LabKey)
LabKey Software produces the CPAS LIMS system, which incorporates some components of the TPP. The LabKey team has also contributed important code to the TPP's code base and plays a role in TPP support.
Proteus (Genologics)
Genologics produces a commerical LIMS systems called Proteus which is compatible with the TPP.
YPED
The Yale Protein Expression Database uses the TPP for data processing.
