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- TPP:7.0.0 Release Notes (6764 bytes)
24: ...rters. This is potentially inefficient for legacy software that calls readHeader() and readPeaks() independe...
36: ...m probability for analysis to 0, to allow the new iProphet NSM model using ptm information content to use al...
43: === [iProphet:] === - Software:ProteinProphet (6941 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
5: ... an integral part of the Trans-Proteomic Pipeline software distribution.
28: IPROPHET: input is from iProphet
40: ... input pepXML file(s) were created by iProphet. ''iProphet is not yet released to the public''. - Software:TPP (8915 bytes)
8: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio]]
9: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:XPRESS]]
10: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:Libra]]
11: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:SBEAMS]]
14: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet]] - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11579 bytes)
84: ...the compilation failed. Perhaps some prerequisite software is not installed on your system. If you can't fig...
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)
3: ... installer is at [http://tools.proteomecenter.org/software.php].
9: ...e tremendous improvement in computer hardware and software over the past decade, this step often remains the...
41: * iProphet support
85: ...omponent of the Trans Proteomic Pipeline suite of software. Although it can be used alone without other TPP ...
101: ...s installed, SpectraST can also be run from the [[Software:Petunia|Petunia]] web interface, with limited opt... - Expert search and TPP usage (12929 bytes)
74: ...ey reflect my incomplete understanding of the TPP software.
356: - iProphet and MHT confidence scores are good. Let’s use t... - Building Peptide Atlas (26978 bytes)
1: ...page outlines the body of [[PeptideAtlas software|software associated with PeptideAtlas]].
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, - TPP:4.2.1 Release Notes (3668 bytes)
7: ...f you have a previously installed version of this software, uninstall the older version (from the start menu...
28: ==iProphet==
29: *Fix page display for iProphet result.
30: *Added unique peptide sequence option for iProphet - TPP:4.3.0 Release Notes (13496 bytes)
6: ...nstalls and configures the TPP and other required software (such as a webserver). For advanced users who ne...
65: * added charge state prediction software
73: Mayu: adding Lukas Reiter's software to calculate decoy-estimated PSM, peptide, and pr...
75: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:Mayu
232: * Tuning iProphet - TPP:4.4.0 Release Notes (31941 bytes)
5: ...nstalls and configures the TPP and other required software (such as a webserver). For advanced users who ne...
183: initial commit of "PepC: Proteomics software for identifying differentially expressed proteins...
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. - TPP:4.5.0 Release Notes (8358 bytes)
3: ...nstalls and configures the TPP and other required software (such as a webserver). For advanced users who ne...
10: * New iModelParser.cgi tpp; fpr viewing iProphet models.
61: * iProphet
79: ** Added IPROPHET option to ProteinProphet
117: * iProphet - TPP:4.5.1 Release Notes (4270 bytes)
4: ...nstalls and configures the TPP and other required software (such as a webserver). For advanced users who ne...
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)
64: == Getting the TPP Software == - ReleasePlanning (12743 bytes)
162: * Write (TPP) software version used in pepXML, protXML, etc
183: * Fix iProphet models page ("performance" models are missing)
204: * PepXMLViewer: no pep-pro probability link in iProphet results - TPP SEWW Demo2012 (29568 bytes)
23: ...ions at [http://wrapper.tanukisoftware.org Tanuki Software] to download the executable ''Jetty-Service.exe''
258: ...r.org/wiki/index.php?title=Image:iprophet.JPG IMG:iprophet] - TPP:4.5.2 Release Notes (4692 bytes)
3: ...nstalls and configures the TPP and other required software (such as a webserver). For advanced users who ne...
39: * Correct issue with iProphet probability filtering and naming of columns.
49: == Getting the TPP Software ==
58: * For guides to installing and using our software, please see our wiki:
59: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:TPP" - TPP:4.6.2 Release Notes (2282 bytes)
3: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
27: == Getting the TPP Software ==
36: * For guides to installing and using our software, please see our wiki:
37: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:TPP" - TPP:4.6.3 Release Notes (4087 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
11: * Addition of FPKM models in ''iProphet'' and ''ProteinProphet''
25: ... Performance enhancements to ''PTMProphet'' and ''iProphet''
68: == Getting the TPP Software ==
77: * For guides to installing and using our software, please see our wiki: - TPP Tutorial (17174 bytes)
7: Commercial software not part of TPP*
11: ...neering. Also, this tutorial does not require any software or data that is not easily available on the web a...
119: == 8. Further peptide-level validation iProphet ==
121: :''iProphet'' (or ''InterProphet'') is a tool that provides s...
123: ...Pipeline'' section in ''Petunia'' to access the ''iProphet'' interface. - TPP:4.7.0 SVN Log (41695 bytes)
84: Fix the name of our own software
799: Add start scan back as a sortable column. Allow iProphet results to link out to the correct search_summary...
812: iProphet: Added optional LENGTH model, and reporting of es...
816: iModelParser.cgi: added display of iProphet estimates of total correct PSM and total correct ... - TPP:4.7.0 Release Notes (9008 bytes)
2: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
66: * InterProphetParser ('''iProphet'''):
70: ** added display of iProphet estimates of total correct PSM and total correct ...
76: ** Allow iProphet results to link out to the correct search_summary...
138: == Getting the TPP Software ==
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