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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==
50: Requests for changes to the pepXML schema should be submitted to the spctools-dev ma...
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- Main Page (6445 bytes)
14: ...erview|SPC open proteomics data formats]]: mzXML, pepXML, protXML==
15: ...include [[Formats:mzXML|mzXML]], [[Formats:pepXML|pepXML]], and [[Formats:protXML|protXML]] on the [[Forma...
44: ...AM-Digestor integrates TIQAM-PeptideAtlas output, pepXML files, and other data in order to select transiti... - TPP:V5Feedback (11460 bytes)
44: ** pvalue link to interact-pval.png is broken. (look in PValueModel.cxx)
49: ...link to view the spectrum in comet results in the pepxmlviewer results in a bad url error</s>
51: * <s>Clicking on the ions link in the comet pepxml view of the top 5 matching peptides results in a ...
53: * <s>Clicking on the 'st' in the pepxmlviewer to view the spectrast results at peptideatl...
70: * <s>Export spreadsheet from pepxmlviewer doesn't seem to do anything ''Joe: nevermin... - Software:Prequips (1386 bytes)
1: [[Image:Prequips_icon.png|thumb|Prequips logo.]]
5: ...formation. Currently data can be read from mzXML, pepXML, Bioworks (tabular), and protXML files. - TPP:Developer Documentation (23931 bytes)
33: ...ll Parser programs (children of Parser.cxx) parse pepXML and protXML with the constrain that all text be e...
69: *libpng www.libpng.org
203: ====Converting search engine results to pepXML format====
204: Analysis programs begin with a pepXML-format file called 'summary.xml', containing the ...
251: ===Converters to pepXML=== - TPP:Files and Formats (299 bytes)
4: ;pepXML: interchange of peptide-level data; ISB-developed - TPP:7.0.0 Release Notes (6884 bytes)
66: === [PepXMLViewer.cgi:] ===
107: ...owing up properly when xl_type is not recorded in pepXML, reported by Zhi - Software:ProteinProphet (6941 bytes)
13: NOPLOT: do not generate plot png file
40: ...inProphet should be used if and only if the input pepXML file(s) were created by iProphet. ''iProphet is n... - Software:Pep3D (1087 bytes)
8: ... identifications are available via an INTERACT or pepXML Viewer interface with PeptideProphet results, seq... - Software:TPP (8915 bytes)
18: ... [[http://tools.proteomecenter.org/formats/pepXML/pepXML_xmlspy_docs.html]]
32: |[[Image:Info.png|middle|left]]
105: ===Input Processing: Search-Engine to pepXML converters=== - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
231: ...data/tests/QuickYeastUPS1/interact.ipro.pep.xml [ PepXML ]
234: - Go back to the PepXML Viewer tab - TPP:Example data analysis (2562 bytes)
19: ===== Converting Searched Data to pepXML =====
20: ...he HTML search results must first be converted to pepXML format for further analysis with the TPP.
24: ## Click on the '''pepXML''' tab.
25: # In the first pane, ''"File(s) to convert to pepXML"'', click on the ''"Add Files"'' button.[[Image:P...
32: # Click on the '''Convert to PepXML''' button in the fourth pane, ''"Convert!"''. - 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==
50: Requests for changes to the pepXML schema should be submitted to the spctools-dev ma... - Formats:Overview (422 bytes)
4: *[[Formats:pepXML|pepXML]]: pepXML is used for storing information about peptide seq... - Software:Out2XML (2805 bytes)
5: ...ool converts Sequest result files (.out files) to pepXML files suitable for use in the TPP.
13: ... .out (sequest search result) files, as well as a pepXML (.xml) file.
20: This will create a pepXML file called:
39: ... this link in all OUT files. Finally,it creates a pepXML file using Out2XML. - 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 - TPP:X!Tandem and the TPP (5454 bytes)
14: ...onverter) to correctly assign scan numbers to the pepXML scan attributes, important for the quantitation t...
34: ...ndem2XML]] is used to convert Tandem results into pepXML. Please see that page for instructions. - TPP:Mascot and the TPP (957 bytes)
23: * Convert MASCOT search results to pepXML with "Mascot2XML <file.dat> -D<full/path/to/datab... - Software:Tandem2XML (1413 bytes)
7: ...eline. This tool converts Tandem result files to pepXML files suitable for use in the TPP.
20: This will create a pepXML file called:
24: ...p?title=Software:XPRESS XPRESS], in the resulting pepXML file: - Software:SpectraST (70083 bytes)
118: * [[Formats:pepXML|.pepXML]] format
154: ...he corresponding experimental spectrum. (If the .pepXML file is created with TPP tools, this should not b...
155: ...ent. For this purpose, it is preferable that the .pepXML has been processed with [[Software:PeptideProphet...
157: ...from a .pepXML file, SpectraST scans through the .pepXML file for confident identifications, and attempts ...
193: !Dataset Identifier!!pepXML Files!!mzXML Files - Spectrast.params (3605 bytes)
7: # A database file to be included in .pepXML outputs for downstream TPP processing - replace w...
29: # Output file format: pepXML or xml (pepXML format), txt (fixed-width text), or xls (tab-deli...
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