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- Formats:protXML (124 bytes)
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- Main Page (6445 bytes)
14: ...PC open proteomics data formats]]: mzXML, pepXML, protXML==
15: ... [[Formats:pepXML|pepXML]], and [[Formats:protXML|protXML]] on the [[Formats:Overview|Formats]] page. - Software:Prequips (1386 bytes)
5: ... read from mzXML, pepXML, Bioworks (tabular), and protXML files. - Prequips:Wishlist (444 bytes)
3: ...matic loading of all meta information in pep- and protXML files<br>--[[User:Gehlenbo|Gehlenbo]] 12:05, 7 Au... - TPP:Developer Documentation (23931 bytes)
33: ...rograms (children of Parser.cxx) parse pepXML and protXML with the constrain that all text be enclosed with...
349: Compacts either pepXML or protXML, combining together start and end tags when no el... - TPP:Files and Formats (299 bytes)
5: ;protXML: interchange of protein-level data; ISB-developed - TPP:7.0.0 Release Notes (6884 bytes)
15: * Updated protXML schema to v10
109: === [ProtXMLViewer] === - Software:ProteinProphet (6941 bytes)
52: Proteins are clustered into groups within the protXML element <protein group>. Usually there is just on...
58: ...independent evidence to earn its own entry in the protXML file." - Software:TPP (8915 bytes)
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
19: ...[[http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html]] - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
2: |[[Image:alert.jpg|middle|left]]
244: ...cal/data/tests/QuickYeastUPS1/interact.prot.xml [ ProtXML ] - Formats:Overview (422 bytes)
5: *[[Formats:protXML|protXML]]: protXML contains proteins and their statistics, as a resu... - TPP Tutorial v1 (43187 bytes)
19: [[image:Pipeline_Tutorial.jpg]]
212: [[Image:sequest_params.jpg]]
327: [[Image:ProbXcorr.jpg]]
397: [[Image:protxml.png]]
399: ...g at a similar but different viewer. This is the protXML viewer. A different viewer is used because the d... - Software:SuperHirn (11737 bytes)
1: [[Image:SuperHirnLogoThumb.jpg|right]]
11: * parsing of protXML data updating MS/MS ids with ProteinProphet proba...
36: [[Image:Prot.jpg|left]] - Expert search and TPP usage (12929 bytes)
22: Paths are hardcoded within pepXML and protXML files. If you move these files, you must run the ... - Terry's compbio links (11123 bytes)
183: ...proteomecenter.org/formats.php Specifications for protXML, pepXML, and more] - Building Peptide Atlas (26978 bytes)
52: ProtXML inherits protIDs from biosequence set.
71: ...of the TPP, adjusts pepXML probabilities based on protXML info, gathers all PSMs (peptide-spectrum matches)...
89: # nsp adjusted probability from protXML
90: # n_adj_obs from protXML
91: # n_sibling_peps from protXML - NewFrontPage (4627 bytes)
27: ... [[Formats:pepXML|pepXML]], and [[Formats:protXML|protXML]], on the [[Formats:Overview|Formats]] page. - TPP:4.2.0 Release Notes (4364 bytes)
38: **protXML schema updated to revision 6; adds optional calcu...
47: **Gzipped (.gz) pepXML, protXML and mzXML or mzML files are now treated as native...
50: ...ig.pl allows for making gzipped mzXML/mzML/pepXML/protXML the default
51: ...and the pipeline will know to gzip the pepXML and protXML files it produces.
68: ...eptide forms as indistinguishable_peptides in the protXML file. - TPP:4.2.1 Release Notes (3668 bytes)
39: ==ProtXML display== - TPP Tutorial v2 (15736 bytes)
95: ...mecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which shows graphically how succes...
106: ...oteomecenter.org/wiki/index.php?title=Image:Pep3D.JPG IMG:Pep3D]
117: ...omecenter.org/wiki/index.php?title=Image:iprophet.JPG IMG:iprophet]
150: ...er.org/wiki/index.php?title=Image:Protxml.JPG IMG:Protxml] - PeptideAtlas software (2240 bytes)
11: ...), updateAllPaths.pl (used when moving pepXML and protXML files to new directories), showProteins.pl (summa...
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