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- 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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