Support for a proteomics and mass spectrometry datatypes for Galaxy
The datatypes in this package are now part of core galaxy. Any packages that depend on these datatypes should remove that dependency.
Migration notes
- The RAW class is changing to ThermoRAW
- Display applications in this package are no longer supported.
| Class | Extension | Sniffer | Application or Purpose |
|---|---|---|---|
| Binary | cps | False | SearchGUI / PeptideShaker |
| PepXML | raw_pepxml | True | TPP Search Engine Outputs |
| PepXML | peptideprophet_pepxml | True | TPP PeptideProphet Outputs |
| PepXML | interprophet_pepxml | True | TPP iProphet Outputs |
| ProtXML | protxml | True | TPP ProteinProphet Outputs |
| GenericXML | trafoxml | False | OpenMS RT Transforms |
| GenericXML | qcml | False | OpenMS QC Data |
| PepXmlReport | pepxml.tsv | False | Tabular PepXML |
| ProtXmlReport | protxml.tsv | False | Tabular ProtXML |
| MascotDat | mascotdat | False | Raw Mascot Search Results |
| MzML | mzml | True | Raw Mass Spec Data |
Mgf IdpDB |
mgf idpdb |
True False |
MS/MS Spectra |
| Wiff | wiff | False | Raw Mass Spec Data |
| MzXML | mzxml | True | Raw Mass Spec Data |
| MzQuantML | mzq | True | HUPO standard for quant data |
| MzIdentML | mzid | True | HUPO standard for ID data |
| TraML | traml | True | HUPO standard for transition lists |
| FeatureXML | featurexml | False | OpenMS |
| ConsensusXML | consensusxml | False | OpenMS |
| IdXML | idxml | False | OpenMS |
| TandemXML | tandem | False | XTandem output |
| RAW | raw | False | Raw Mass Spec Data |
| Msp | msp | True | Spectral Library |
| SPLib | splib | True | Spectral Library |
| Ms2 | ms2 | False | MS/MS Spectra |
| XHunterAslFormat | hlf | False | Spectral Library |
This package also installs display applications for mzML, PepXML and ProtXML formats. These are designed to work with the protviz web application. Configuring this application requires a fair number of extra steps though. See the protviz documentation for more info.