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- TPP:Sequest and the TPP (1847 bytes)
1: ==What is Sequest?==
2: Sequest is a commercial, closed-source search engine, ori...
4: ==Using Sequest and the TPP==
5: ...ive instructions for various ways of working with Sequest and the TPP. For example, someone could write in...
8: ... be different in more recent versions of Bioworks SEQUEST.
Page text matches
- TPP:Supported Search Engines (1578 bytes)
14: ===[[TPP:Sequest and the TPP|SEQUEST]]===
15: [http://fields.scripps.edu/sequest/ SEQUEST] is a commercial search engine, currently sold by... - TPP:Developer Documentation (23931 bytes)
207: *For SEQUEST results, you must specify the sequest.params file used for the search:
208: ...th summary.html and summary.mzXML (as well as the SEQUEST results .tgz or subdirectory), type:
209: Sequest2XML summary.html -Psequest.params
255: ====Sequest2XML====
259: Sequest2XML summary.html (-P/full/path/mysequest.params) (-M) (-m) (-a) (-pI) (-Eenzyme) - Software:Overview (3074 bytes)
52: [[Software:SPE|SPE]]: SEQUEST Parameter Editor tool - TPP:Files and Formats (299 bytes)
2: ...containing peptide assignment (from MS/MS input); SEQUEST output - Software:XPRESS (1756 bytes)
8: ... are then updated in the INTERACT list. For those SEQUEST users interested in using the software, ThermoFin... - Software:TPP (8915 bytes)
86: Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready...
93: ...ML2Search|MzXML2Search]]: Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files
106: *Sequest results: [[Software:Out2XML|Out2XML]]
115: The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF... - TPP:Example data analysis (2562 bytes)
11: ==== Sequest Searched Data Example ====
20: ...ample data you've downloaded was searched with '''Sequest''' using the ''runsearch'' tool. The ''runsearch...
22: # On the '''Home''' tab make sure that the ''Sequest'' analysis pipeline is selected.
28: # In the second pane, ''"Specify Sequest Parameters File"'', click on the ''"Add Files"'' ...
30: ## Select the ''sequest.params'' file in this directory and click on the ... - Software:SPE (46 bytes)
1: '''SPE: SEQUEST Parameter Editor''' - Formats:pepXML (2274 bytes)
37: Sequest: [[Software:Out2XML|Out2XML]] - Formats:mzXML (9722 bytes)
39: | .dta || sequest || dta2mzXML || yes || in TPP release || refer to...
77: ... table. This format was originally developed for Sequest. No annotation metadata is stored in this format...
114: * out2linux.pl: working with Bioworks Sequest output. See [[Software:Out2XML]] page. - Software:Out2XML (2805 bytes)
5: ...t of the processing pipeline. This tool converts Sequest result files (.out files) to pepXML files suitabl...
11: ===Converting Sequest results to TPP input files===
13: ...tgz archive of all .dta (spectra input) and .out (sequest search result) files, as well as a pepXML (.xml) ...
35: out2linux.pl is a programm intended to help with Sequest search using Bioworks Browser on a Windows comput...
39: out2linux.pl creates a new params file called sequest.params based on the existing params file and conv... - TPP:Sequest and the TPP (1847 bytes)
1: ==What is Sequest?==
2: Sequest is a commercial, closed-source search engine, ori...
4: ==Using Sequest and the TPP==
5: ...ive instructions for various ways of working with Sequest and the TPP. For example, someone could write in...
8: ... be different in more recent versions of Bioworks SEQUEST. - Software:SpectraST (70083 bytes)
17: ...ries) on a modern personal computer. In contrast, SEQUEST, one of the most popular sequence search engine, ...
111: * .dta (SEQUEST) format, a simple peak list preceded by precursor...
195: |Alpha||A-SEQ.xml (SEQUEST results of A1.mzXML),<br>A-MAS.xml (Mascot result...
197: ...|B1.xml (SEQUEST results of B1.mzXML),<br>B2.xml (SEQUEST results of B2.mzXML)||B1.mzXML,<br>B2.mzXML
199: |Gamma||G.xml (combined SEQUEST results of all .mzXML files)||G1.mzXML,<br>G2.mzX... - Spectrast create.params (4398 bytes)
105: # Set the minimum SEQUEST deltaCn value for a spectrum to be included
145: # Choices are SN (signal-to-noise), XCORR (SEQUEST Xcorr), PROB (probability) - TPP Tutorial v1 (43187 bytes)
15: ...signed for the scientist who is currently running SEQUEST searches on their tandem mass spectrometry data a...
113: ... SEQUEST so that the user does not need to have a SEQUEST license for the computer that is used for this tu...
129: ..., folders that contain the .out and .dta files, a sequest.params file and a folder containing a FASTA datab...
145: =SEQUEST data analysis=
157: ...EST, Mascot, Tandem or SpectraST. The default is SEQUEST which is what will start with in this tutorial. ... - TPP:Related Tools (6244 bytes)
44: ===SEQUEST===
45: [http://fields.scripps.edu/sequest/ SEQUEST] is a commercial search engine, currently sold by... - Software:Out2Summary (104 bytes)
1: Convert Sequest and TurboSequest *.out files into a single HTML-SUMMARY file ready... - Expert search and TPP usage (12929 bytes)
98: and generate parameters files for X!Tandem, SEQUEST, and Myrimatch. Here is how to use it:
111: In place of Tandem you can type Sequest or Myrimatch. - Terry's blog (18394 bytes)
49: ...e Urine PeptideAtlas, which proteins were ID'd by SEQUEST and X!Tandem that were missed by SpectraST?
50: ...tified spectra (TMF inserted this) 4. Search with SEQUEST, X!Tandem, or other engine(s) that compare agains...
93: ... consider ID continuity so we don't double model. SEQUEST does not. X!Tandem? Ask Henry.
120: * SEQUEST already considers consecutiveness of peak IDs in ... - Building Peptide Atlas (26978 bytes)
14: ...the spectra with a database search engine such as SEQUEST, X!Tandem, or SpectraST, then validating the hits...
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