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- Formats:pepXML (2274 bytes)
1: ...erters are available to transform output files to pepXML.
3: ==PepXML Schema ==
7: ...eforge.net/schema_revision/pepXML/pepXML_v123.xsd pepXML 1.23 Schema] (xsd)
35: ==Search-Engine to pepXML converters==
44: == Related Formats ==
Page text matches
- Main Page (6427 bytes)
14: ...erview|SPC open proteomics data formats]]: mzXML, pepXML, protXML==
15: ...rmats:protXML|protXML]] on the [[Formats:Overview|Formats]] page.
22: * conversion of raw data to open formats;
44: ...AM-Digestor integrates TIQAM-PeptideAtlas output, pepXML files, and other data in order to select transiti... - TPP:7.0.0 Release Notes (6884 bytes)
25: ... MZP_MZ5), which will include support for all HDF formats (MZ5 and mzMLb). Note that mzMLb.gz is not yet su...
66: === [PepXMLViewer.cgi:] ===
107: ...owing up properly when xl_type is not recorded in pepXML, reported by Zhi - Software:TPP (8918 bytes)
17: ...p://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML]]
18: ... [[http://tools.proteomecenter.org/formats/pepXML/pepXML_xmlspy_docs.html]]
19: ...77 333 1168 300 [[http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html]]
105: ===Input Processing: Search-Engine to pepXML converters=== - Formats:pepXML (2274 bytes)
1: ...erters are available to transform output files to pepXML.
3: ==PepXML Schema ==
7: ...eforge.net/schema_revision/pepXML/pepXML_v123.xsd pepXML 1.23 Schema] (xsd)
35: ==Search-Engine to pepXML converters==
44: == Related Formats == - Formats:Overview (422 bytes)
1: These open formats were created at the ISB/SPC for the purposes of s...
3: *[[Formats:mzXML|mzXML]]: mzXML is used for storing spectra-...
4: *[[Formats:pepXML|pepXML]]: pepXML is used for storing information about peptide seq...
5: *[[Formats:protXML|protXML]]: protXML contains proteins and ... - Software:Mascot2XML (2806 bytes)
5: Converts Mascot search results in .dat files to pepXML (.xml) format.
8: ...2XML''' coverts Mascot-specific search results to pepXML.
13: ..., under the Mascot mode --> Analysis Pipeline --> pepXML
21: ... -html : generate html output (default output is pepXML)
24: -desc : generate protein description in pepXML output - Software:SpectraST (70083 bytes)
66: ... Importing libraries from X!Hunter and BiblioSpec formats
93: ...reates a searchable spectral library from various formats to prepare for searching. In the latter, SpectraS...
97: ...spectrast <options> <list of files of appropriate formats></code>
105: ...erform spectral searching from the following data formats:
108: * [[Formats:mzXML|.mzXML]] (all versions) format - TPP Tutorial v1 (43187 bytes)
23: ... mzXML and mzDATA are instrument independent data formats used by data analysis software like TPP and data ...
160: ==Creating pepXML Files==
161: ...he next step will be to convert the .out files to pepXML files.
163: ... used to search the data. We will start with the pepXML tab.
165: ...dem results. Also, the Mascot software contains a pepXML exporter. - TPP:Related Tools (6244 bytes)
2: ...ial. Some of these tools provide compatible data formats that can be used as input to the TPP, while other...
4: ...pectrometer Instrument-Specific Software and File Formats==
10: ...e [[Formats:mzXML]] for an overview of compatible formats and converter software.
14: |+ Compatible Mass-Spec file formats
27: ==Compatible Mass-Spectroscopy Input File Formats== - Software:TIQAM (7374 bytes)
10: ... To prioritize peptides which should be targeted, pepXML files or tables (format: peptide, number) can be ...
18: TIQAM expects the following data formats:
19: * Centroided [[Formats:mzXML|mzXML]] data (use [http://web.bii.a-star.ed...
21: * pepXML files. This file is generated by the [[Software:T...
84: ...let us know] and we will work with you to get the formats compatible. - TPP Tandem search (19915 bytes)
25: [[Formats:mzXML | mzXML]] is a instrument independent data ...
240: ...n the “Analysis Pipeline (Tandem)” and the “pepXML” tab.'''
241: '''Under “Files to convert to pepXML”, click “Add Files” and select the six .tan...
243: After this is done, '''Click “Convert to PepXML” at the bottom.
245: [[Image:convertpepxml.png]] - NewFrontPage (4627 bytes)
27: ...mats:protXML|protXML]], on the [[Formats:Overview|Formats]] page.
38: ... mainly containing useful information about the [[Formats:mzXML|mzXML]] format. - TPP:4.2.0 Release Notes (4364 bytes)
26: *pepXMLViewer:
39: **pepXML schema updated to revision 13; adds charge states...
47: ...and mzXML or mzML files are now treated as native formats, for reduced disk usage and easier sharing across...
50: ...ui_config.pl allows for making gzipped mzXML/mzML/pepXML/protXML the default
51: ...t filename and the pipeline will know to gzip the pepXML and protXML files it produces. - PeptideAtlas software (2240 bytes)
10: ...l before building PeptideAtlas -- converting file formats and searching -- but some of it is useful during ...
11: ...ctories), showProteins.pl (summary of proteins in pepXML). - TPP:4.4.0 Release Notes (31941 bytes)
12: ... project. This tool supports all the same native formats as the previous tools, is better supported, and i...
14: === pepXML schema ===
16: * New pepXML 1.15: Adds more search engines (ProteinPilot, Pro...
100: [ASAPRatioProteinRatioParser] Implement PepXML cacheing as XPRESS
187: ...escriptions containing reserved XML characters in pepXML output - TPP:4.5.0 SVN Log (242349 bytes)
10: ...es/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXIndexFile.cxx
12: PepXMLViewer.cgi: Update index version
28: ...es/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXOptions.cxx
30: PepXMLViewer.cgi: Fix bug on commandline generated index...
41: ...es/4-5/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXFilter.cxx - TPP:4.7.0 SVN Log (41695 bytes)
76: ...hen no matched ions information is available from pepXML
80: [PepXMLViewer] Display MSGF+ and (correct) Myrimatch sear...
162: * Added comet-pepxml.cgi to Windows installer so it gets installed.
163: * Fixed the link in the PepXMLViewer to use the pep.xml file instead
341: formats, as Mingw/Win32 passes the call to a Window's lib... - Citing the TPP (8463 bytes)
21: ...s MS/MS analysis platform utilizing open XML file formats''
185: == Mass Spectrometry File Formats in General ==
187: ''File formats commonly used in mass spectrometry proteomics''
196: == pepXML and protXML Initial Paper ==
198: ...s MS/MS analysis platform utilizing open XML file formats''
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