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- TPP:Supported Search Engines (1578 bytes)
1: ==what is a search engine?==
2: In this context, a "search engine" is a tool that attempts to assign a pepti...
5: ==supported search engines==
6: The TPP now officially works with these search engines:
9: ...t-ms.sourceforge.net/ COMET] open-source database search engine provided with TPP (as of version 4.7.1) - Expert search and TPP usage (12929 bytes)
1: This is a guide to searching and running the TPP on MS/MS data from within ...
12: ...rchive/<investigator>/<project>/<experiment_tag>/<search_descriptor>
17: ...nderscore, and a brief descriptor of the database searched.
19: ... results and TPP results should be stored in the <search_descriptor> directories.
25: == Search and TPP == - TPP Tandem search (19915 bytes)
1: =Performing XTandem search using the Trans Proteomic Pipeline (TPP) Tutorial...
12: ...teps: using TPP to perform a database search. The search engine X!Tandem will be used in this tutorial as ...
16: ...net Explorer or Firefox is required. Although the search engine [http://www.thegpm.org/TANDEM/ X!Tandem] ...
73: ...tutorial is written from the point of view of a researcher viewing data on the computer where the TPP tool...
79: ==Database search using X!Tandem== - Alt NxST search strategy (1763 bytes)
1: ...w.peptideatlas.org/upload/Atwood-York_GlycopeptideSearchStrategy.pdf, but has been modified to work with t...
11: # create search database with NxS/T changed to NBS/T. This will
16: # Make search directory
26: ln -s /data2/search/yzhou/CP/LCQ/Prostate_*.mzXML .
34: # Substitute search settings
Page text matches
- Main Page (6445 bytes)
1: ... projects in support of cutting-edge proteomics research. The SPC maintains active support and education ...
23: ...rceforge.net/ Comet], as well as spectral library searching with [[SpectraST]], and cross-linking data wit...
24: * conversion of search engine results to a unified format;
66: ...al other organisms, and searched using the latest search
68: searching are subsequently processed through the Trans P... - TPP:V5Feedback (11460 bytes)
74: * <s>Can't remove mzML files from processing search form</s>
76: ... pepxmlviewer when viewing results of a spectrast search result in: - Prequips:Eclipse Setup (5641 bytes)
20: ...ware Updates > Find and Install ...'''. Select '''Search for new features to install''' and then select ''... - MS level 2 (326 bytes)
1: ...m assignment|manually]] or automatically with a [[search engine]]. - TPP:Supported Search Engines (1578 bytes)
1: ==what is a search engine?==
2: In this context, a "search engine" is a tool that attempts to assign a pepti...
5: ==supported search engines==
6: The TPP now officially works with these search engines:
9: ...t-ms.sourceforge.net/ COMET] open-source database search engine provided with TPP (as of version 4.7.1) - TPP:Developer Documentation (23931 bytes)
201: ...==Assigning peptide sequences to spectra (using a search engine)====
203: ====Converting search engine results to pepXML format====
204: ...y.xml', containing the peptides identified by the search engine.
207: ...must specify the sequest.params file used for the search:
211: ...t results, you must specify the database used for search: - Software:Overview (3074 bytes)
9: ...mary|Out2Summary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]],
32: [[Software:ProbID|ProbID]]: open-source search engine - TPP:Frequently Asked Questions (5647 bytes)
57: ...All TPP users are highly encouraged to subscribe, search the archives, and post their questions here for a...
76: '''Journal of Proteome Research 2023 22 (2), 615-624'''; - TPP:7.0.0 Release Notes (6884 bytes)
41: ...RNINGS when user doesn't specify all mods used in search at runtime of PTMProphet.
80: * Honor selected queue for non-search jobs! - Software:PeptideProphet (1728 bytes)
5: ...ol for generating statistical validation of MS/MS search engines' spectra-to-peptide sequence assignments....
8: ...liminating the need to manually validate database search results. In addition, it can facilitate the bench...
11: ...eptide identifications made by MS/MS and database search." Anal Chem 74:5383-92. [http://tools.proteomecen... - Software:ProteinProphet (6941 bytes)
40: ...ptideProphet results from several experiments and search engines. The IPROPHET option to ProteinProphet sh... - Software:TPP (8915 bytes)
59: ...deProphet]]: Statistical validation of PSMs using search engine results.
61: ...results; can also combine the results of multiple search engines.
82: ===Spectral Library Building and Searching===
83: ... spectra. Builds spectral libraries from sequence search results.
93: [[Software:MzXML2Search|MzXML2Search]]: Converts mzXML files to SEQUEST dta, MASCOT mg... - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
175: ...to test your installation with a very quick Comet search and a PeptideProphet->iProphet->ProteinProphet->m...
209: - (Save Search Parameters File)
212: [TPP Tools] [Comet Search]
219: [Run Comet Search] - TPP:Example data analysis (2562 bytes)
11: ==== Sequest Searched Data Example ====
14: ...tp://tools.proteomecenter.org/sample_data/raftapr_searched.tgz
19: ===== Converting Searched Data to pepXML =====
20: ...y MS run (mzXML) file that is searched. The HTML search results must first be converted to pepXML format ... - Software:PeptideSieve (6357 bytes)
8: ...tein identification scoring functions of database search software, providing a panel of reagents for prote... - Formats:pepXML (2274 bytes)
1: ...s and subsequent peptide-level analyses. Several search engines already have native support for outputtin...
26: ** Adds "X! Tandem (k-score)" search engine
28: ** Adds search_engine attribute to msms_run_summary
31: ** Schema updated to include omssa and myrimatch search engine names
35: ==Search-Engine to pepXML converters== - Formats:mzXML (9722 bytes)
29: ...nverter || [http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html external link]
85: ...other simple text format developed for the Mascot search engine.
96: ...yMsXML.html http://www.umiacs.umd.edu/~nedwards/research/PyMsXML.html]
99: ===MzXML2Search===
130: ...ometry Data and its Application in a Proteomics Research Environment." Nature Biotechnology 22(11):1459-14... - Software:Out2XML (2805 bytes)
13: ...ive of all .dta (spectra input) and .out (sequest search result) files, as well as a pepXML (.xml) file.
35: ...er and TPP on a Linux server. When performing the search with Bioworks browser, the params file as well as...
43: 1. Perform Sequest search using Bioworks browser.
47: 3. Transfer DB used for the search to your DBs location on the Linux server. - TPP:Installing on Ubuntu 7.04 (9446 bytes)
22: below. You can find them for Ubuntu using the search feature of this webpage: - Software:Mascot2XML (2806 bytes)
5: Converts Mascot search results in .dat files to pepXML (.xml) format.
8: ...esults. '''Mascot2XML''' coverts Mascot-specific search results to pepXML.
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