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8
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1 Proteomics Datatypes
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2 ====================
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3
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4 Support for a proteomics and mass spectrometry datatypes for Galaxy_
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5
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6 .. _Galaxy: http://galaxyproject.org/
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7
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8
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9 Included Datatypes
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10 ------------------
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11
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12 ================ ===================== ======= ====================================
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13 Class Extension Sniffer Application or Purpose
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14 ================ ===================== ======= ====================================
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15 Binary cps False SearchGUI_ / PeptideShaker_
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16 PepXML_ raw_pepxml True TPP_ Search Engine Outputs
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17 PepXML_ peptideprophet_pepxml True TPP_ PeptideProphet Outputs
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18 PepXML_ interprophet_pepxml True TPP_ iProphet Outputs
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19 ProtXML_ protxml True TPP_ ProteinProphet Outputs
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20 GenericXML trafoxml False OpenMS_ RT Transforms
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21 GenericXML qcml_ False OpenMS_ QC Data
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22 PepXmlReport pepxml.tsv False Tabular PepXML
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23 ProtXmlReport protxml.tsv False Tabular ProtXML
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24 MascotDat mascotdat False Raw Mascot Search Results
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25 MzML_ mzml True Raw Mass Spec Data
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26 Mgf mgf True MS/MS Spectra
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27 IdpDB idpdb False
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28 Wiff wiff False Raw Mass Spec Data
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29 MzXML mzxml True Raw Mass Spec Data
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30 MzQuantML_ mzq True HUPO standard for quant data
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31 MzIdentML_ mzid True HUPO standard for ID data
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32 TraML_ traml True HUPO standard for transition lists
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33 FeatureXML featurexml False OpenMS_
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34 ConsensusXML consensusxml False OpenMS_
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35 IdXML idxml False OpenMS_
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36 TandemXML_ tandem False XTandem output
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37 RAW raw False Raw Mass Spec Data
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38 Msp_ msp True Spectral Library
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39 SPLib_ splib True Spectral Library
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40 Ms2 ms2 False MS/MS Spectra
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41 XHunterAslFormat hlf False Spectral Library
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42 ================ ===================== ======= ====================================
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43
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44
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45 .. _qcml: http://code.google.com/p/qcml
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46 .. _PepXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML
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47 .. _ProtXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML
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48 .. _TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
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49 .. _OpenMS: https://github.com/OpenMS/OpenMS
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50 .. _SearchGUI: https://code.google.com/p/searchgui/
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51 .. _PeptideShaker: https://code.google.com/p/peptide-shaker/
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52 .. _MzML: http://www.psidev.info/mzml_1_0_0%20
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53 .. _MzQuantML: http://www.psidev.info/mzquantml
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54 .. _MzIdentML: http://www.psidev.info/mzidentml
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55 .. _TraML: http://www.psidev.info/traml
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56 .. _TandemXML: http://www.thegpm.org/docs/X_series_output_form.pdf
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57 .. _Msp: http://chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf
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58 .. _SPLib: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Developer.27s_Guide
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59
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60 Visualization
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61 -------------
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62
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63 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.
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64
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65 .. _protviz: https://bitbucket.org/Andrew_Brock/proteomics-visualise
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66
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