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- TPP:7.0.0 Release Notes (6884 bytes)
39: ...m probability for analysis to 0, to allow the new iProphet NSM model using ptm information content to use al...
46: === [iProphet:] === - Software:ProteinProphet (6941 bytes)
28: IPROPHET: input is from iProphet
40: ... input pepXML file(s) were created by iProphet. ''iProphet is not yet released to the public''.
42: ...uperceded by iProphet and should not be used with iProphet. - Software:TPP (8915 bytes)
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
16: ...=TPP_Tutorial#8._Further_peptide-level_validation_iProphet]]
61: [[Software:iProphet|iProphet]]: Distinct peptide sequence validation, using [[...
63: ...deProphet|PeptideProphet]] OR [[Software:iProphet|iProphet]] results. - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
2: |[[Image:alert.jpg|middle|left]]
175: ...h a very quick Comet search and a PeptideProphet->iProphet->ProteinProphet->mzIdentML processing, try this r...
227: - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
241: - Checkmark "Input is from iProphet" - Software:SpectraST (70083 bytes)
41: * iProphet support
155: ...all the search hits have probabilities assigned. (iProphet probabilities are used over PeptideProphet ones i...
723: ...ually look for the .none file, but the resulting .jpg file will be named with the same prefix as the .n... - Expert search and TPP usage (12929 bytes)
356: - iProphet and MHT confidence scores are good. Let’s use t... - Terry's blog (18394 bytes)
4: ====evaluating iProphet on urine data====
22: iProphet all files together
75: ...ps to take toward figuring out how to make use of iProphet:
76: ...easier to adapt createPipelineInput.pl to process iProphet output.
77: ...batches and run iProphet on each separately, have iProphet generate its models based only on a random set of... - Building Peptide Atlas (26978 bytes)
14: ...scripts such as runtandemsearch automatically run iProphet after PeptideProphet.
33: ===Run iProphet===
35: ...each experiment, combine ''per experiment'' using iProphet====
36: ...parallel to the search results directories, named iProphet. Then, for example,
37: $ iProphet ../{XTK,SPC,SEQ}*/interact-prob.pep.xml interact-... - TPP:4.2.0 Release Notes (4364 bytes)
68: ...k MU ( enabled when PROTLEN option is used) , for IPROPHET print alternative peptide forms as indistinguisha...
69: **Improved viewing of iProphet results now displays alternative peptide version ...
70: *iProphet:
76: **New iProphet tab, plus support within xinteract - TPP:4.2.1 Release Notes (3668 bytes)
28: ==iProphet==
29: *Fix page display for iProphet result.
30: *Added unique peptide sequence option for iProphet - 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]
108: == 8. Further peptide-level validation iProphet ==
110: :''iProphet'' (or ''InterProphet'') is a tool that provides s...
112: ...Pipeline'' section in ''Petunia'' to access the ''iProphet'' interface. - TPP:4.3.0 Release Notes (13496 bytes)
232: * Tuning iProphet
261: * Recognize iProphet and show those probabilities when available.
263: * Show iProphet probabilities and results.
267: * Pass through iProphet probabilities and results when available - TPP:4.4.0 Release Notes (31941 bytes)
203: [xinteract] skip the iprophet stuff for LabKey purposes (currently internally i...
406: ...y of the engines used in the analysis (useful for iProphet viewing).
447: InterProphetParser Filter out any old iProphet results from the final output file.
469: ** iProphet support - TPP:4.5.0 Release Notes (8358 bytes)
10: * New iModelParser.cgi tpp; fpr viewing iProphet models.
61: * iProphet
79: ** Added IPROPHET option to ProteinProphet
117: * iProphet
118: ** When the pepXML already contains the iProphet tags filter them out, including the end tag. - TPP:4.5.1 Release Notes (4270 bytes)
14: ...s to pepxml_html2.pl with PepXMLViewer.cgi links (iProphet only...?)
40: ...r.cgi (heading for PeptideProphet Probability and iProphet Probability were both called "probability")
42: * Fixed iProphet models page ("performance" models were missing) - TPP:Installing the Trans-Proteomic Pipeline (TPP) 4.4.0 on Mac OS X 10.6.4 (12202 bytes)
36: - TPP 4.6.1 problems: ions2 / Lorikeet and iProphet (iModelParser.cgi) plots https://groups.google.co... - ReleasePlanning (12743 bytes)
183: * Fix iProphet models page ("performance" models are missing)
204: * PepXMLViewer: no pep-pro probability link in iProphet results - TPP SEWW Demo2012 (29568 bytes)
245: ...mecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which shows graphically how succes...
251: ...oteomecenter.org/wiki/index.php?title=Image:Pep3D.JPG
258: ...r.org/wiki/index.php?title=Image:iprophet.JPG IMG:iprophet]
272: ...eomecenter.org/wiki/index.php?title=Image:Protxml.JPG IMG:Protxml] - TPP WISB Demo2012 (16916 bytes)
211: ...mecenter.org/wiki/index.php?title=Image:PlotModel.JPG IMG:PlotModel] which shows graphically how succes...
218: ...oteomecenter.org/wiki/index.php?title=Image:Pep3D.JPG
225: ...r.org/wiki/index.php?title=Image:iprophet.JPG IMG:iprophet]
239: ...eomecenter.org/wiki/index.php?title=Image:Protxml.JPG IMG:Protxml] - TPP:4.5.2 Release Notes (4692 bytes)
39: * Correct issue with iProphet probability filtering and naming of columns.
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