TPP:Related Tools

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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 compatiable data formats that can be used as input to the TPP, while others repackage or redistribute the TPP itself.


Compatible Mass-Spectrometer Instrument-Specific Software and File Formats

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.


Compatible Mass-Spec file formats
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

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
  • Comet
  • ProbID
  • Mascot
  • X!Tandem
  • Phenyx


Other tools

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 for the IPP InSilicos has contributed important code to the TPP's code base and plays a role in TPP support.

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.

Genologics produces a commerical LIMS systems called Proteus which is compatible with the TPP.

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