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Improved readme
author iracooke
date Sun, 29 Mar 2015 19:24:40 -0400
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1 Proteomics Datatypes
2 ====================
3
4 Support for a proteomics and mass spectrometry datatypes for Galaxy_
5
6 .. _Galaxy: http://galaxyproject.org/
7
8
9 Included Datatypes
10 ------------------
11
12 ================ ===================== ======= ====================================
13 Class Extension Sniffer Application or Purpose
14 ================ ===================== ======= ====================================
15 Binary cps False SearchGUI_ / PeptideShaker_
16 PepXML_ raw_pepxml True TPP_ Search Engine Outputs
17 PepXML_ peptideprophet_pepxml True TPP_ PeptideProphet Outputs
18 PepXML_ interprophet_pepxml True TPP_ iProphet Outputs
19 ProtXML_ protxml True TPP_ ProteinProphet Outputs
20 GenericXML trafoxml False OpenMS_ RT Transforms
21 GenericXML qcml_ False OpenMS_ QC Data
22 PepXmlReport pepxml.tsv False Tabular PepXML
23 ProtXmlReport protxml.tsv False Tabular ProtXML
24 MascotDat mascotdat False Raw Mascot Search Results
25 MzML_ mzml True Raw Mass Spec Data
26 Mgf mgf True MS/MS Spectra
27 IdpDB idpdb False
28 Wiff wiff False Raw Mass Spec Data
29 MzXML mzxml True Raw Mass Spec Data
30 MzQuantML_ mzq True HUPO standard for quant data
31 MzIdentML_ mzid True HUPO standard for ID data
32 TraML_ traml True HUPO standard for transition lists
33 FeatureXML featurexml False OpenMS_
34 ConsensusXML consensusxml False OpenMS_
35 IdXML idxml False OpenMS_
36 TandemXML_ tandem False XTandem output
37 RAW raw False Raw Mass Spec Data
38 Msp msp False Spectral Library
39 Ms2 ms2 False MS/MS Spectra
40 XHunterAslFormat hlf False Spectral Library
41 ================ ===================== ======= ====================================
42
43
44 .. _qcml: http://code.google.com/p/qcml
45 .. _PepXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML
46 .. _ProtXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML
47 .. _TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
48 .. _OpenMS: https://github.com/OpenMS/OpenMS
49 .. _SearchGUI: https://code.google.com/p/searchgui/
50 .. _PeptideShaker: https://code.google.com/p/peptide-shaker/
51 .. _MzML: http://www.psidev.info/mzml_1_0_0%20
52 .. _MzQuantML: http://www.psidev.info/mzquantml
53 .. _MzIdentML: http://www.psidev.info/mzidentml
54 .. _TraML: http://www.psidev.info/traml
55 .. _TandemXML: http://www.thegpm.org/docs/X_series_output_form.pdf
56
57 Visualization
58 -------------
59
60 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.
61
62 .. _protviz: https://bitbucket.org/Andrew_Brock/proteomics-visualise
63