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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 == - TPP:4.7.1 Release Notes (5613 bytes)
2: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
10: * iProphet: Rewrite spectrum_query index to make unique for...
12: * ASAPRatio: Use iProphet probs if present. When running gnuplot test for e...
14: * Petunia (iProphet Page): Add an option to launch ProteinProphet,
15: ** iProphet Page in Petunia can now run PTMProphet and Quanti... - TPP:4.8.0 Release Notes (9645 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
52: ** Added option to run ProteinProphet from iProphet page
86: ...L file in one combination file such as created by iProphet.
99: * iProphet: printing all_ntt_probs twice for ntt=0 caused a ...
123: == Getting the TPP Software == - TPP:5.0.0 SVN Log (143410 bytes)
2146: ...p alignment of various filters and options; added iProphet quick-filter to summary section; expanded size of...
2156: - Moved iProphet probability to first column by default
2157: - Added filter options for all iProphet models and cleaned up options
2158: - Removed obsolete iProphet fields from possible column list
2522: - Provide more feedback when running command (software name, version, and file being analyzed) as well a... - TPP:5.0.0 Release Notes (17167 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
17: ** allows for user-configurable software and data locations
20: * New major software components:
94: ** Link iProphet prob to new models page
95: ** Added iProphet quick-filter to summary section - TPP:5.1.0 SVN Log (66940 bytes)
291: BUGFIX: iProphet NRS model edge condition corrected (missing '-' i...
313: Bring your software dreams to reality with the simple object interfac...
466: ...ose all open ones, when they are nested...prevent iProphet from creating invalid pepXML due to unclosed anal...
663: ...een modified peptide sequence representation from iProphet and PeptideProphet.
1136: iProphet: fix a bug with small sized runs. - TPP:5.1.0 Release Notes (19616 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
176: ...and Kojak scores to possible columns when viewing iProphet results
272: * ''iProphet''
402: = Getting the TPP Software =
411: * For guides to installing and using our software, please see our wiki: - Tutorial:StPeter1 (3074 bytes)
5: ...torial provides basic instruction on the use of [[Software:StPeter|StPeter]] for label-free quantification o...
37: ...eProphet]], [[Software:iProphet|iProphet]], and [[Software:ProteinProphet|ProteinProphet]].
46: ** Under IPROPHET OPTIONS:
47: *** Select ''RUN iProphet''
50: ...7 original pepXML files. These ipro files contain iProphet adjusted probabilities for peptide identification... - TPP 5.2.0: Installing on Ubuntu 18.04 LTS (11542 bytes)
85: ...the compilation failed. Perhaps some prerequisite software is not installed on your system. If you can't fig...
225: - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
239: - Checkmark "Input is from iProphet" - Citing the TPP (8463 bytes)
30: == iProphet and Combining Search Results Review ==
32: ''iProphet: multi-level integrative analysis of shotgun prot...
108: ... mass spectrometry and SUMmOn pattern recognition software''
119: ''reSpect: software for identification of high and low abundance ion ... - Running the TPP docker image (8867 bytes)
4: ...s, which can be run on any system with the Docker software installed. The spctools/tpp image is built on the...
140: - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
154: - Checkmark "Input is from iProphet" - TPP:5.2.0 Release Notes (15364 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
118: ...lways show File Output options for ''xinteract'', iProphet'', ''PTMProphet'', and ''ProteinProphet'' pages
136: ** Display list of search engines when viewing ''iProphet'' results
239: * ''iProphet''
328: = Getting the TPP Software = - TPP:6.0.0 Release Notes (38799 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
58: ...single command tool to run comet, PeptideProphet, iProphet, PTMProphet and then export results as xls
298: * ''iProphet''
299: ** Increasing multi-threading ability for iProphet
301: ** BUGFIX prevent a single thread in iProphet multi-threaded mode from disabling and entire mod... - TPP 6.0.0: Installing on Ubuntu 20.04 LTS (11299 bytes)
82: ...the compilation failed. Perhaps some prerequisite software is not installed on your system. If you can't fig...
224: - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
238: - Checkmark "Input is from iProphet" - TPP 6.1.0: Installing on Ubuntu 20.04 LTS (11554 bytes)
84: ...the compilation failed. Perhaps some prerequisite software is not installed on your system. If you can't fig...
228: - Under -IPROPHET OPTIONS- Check box next to "RUN iProphet"
242: - Checkmark "Input is from iProphet" - TPP:6.1.0 Release Notes (11384 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
81: ...e -THREADS= parameter apply to PeptideProphet and iProphet.
211: = Getting the TPP Software =
220: * For guides to installing and using our software, please see our wiki:
221: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:TPP - TPP:6.2.0 Release Notes (15394 bytes)
1: ...nstalls and configures the TPP and other required software (such as a web server). For advanced users who n...
29: *** iProphet
122: * ''iProphet''
284: = Getting the TPP Software =
293: * For guides to installing and using our software, please see our wiki: - TPP 6.2.0: Installing on Ubuntu 22.04 LTS (11582 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" - TPP:6.3.0 Release Notes (8953 bytes)
4: ...ch installs and configures TPP and other required software (such as a web server). For advanced users who n...
29: === iProphet ===
125: * Put PTMProphet options before iProphet options
159: ...ophetParser run on PeptideProphet results, before iProphet instead of after
210: = Getting the TPP Software =
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