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- TPP:Developer Documentation (23931 bytes)
204: ... programs begin with a pepXML-format file called 'summary.xml', containing the peptides identified by the s...
208: In directory with summary.html and summary.mzXML (as well as the SEQUEST results .tgz or sub...
209: Sequest2XML summary.html -Psequest.params
212: In the directory with summary.dat and summary.mzXML, type:
213: Mascot2XML summary.dat -D/full/path/database - Software:TPP (8915 bytes)
86: ...T and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT - TPP:Example data analysis (2562 bytes)
20: ...' tool. The ''runsearch'' tool generates an HTML summary for every MS run (mzXML) file that is searched. ... - Formats:mzXML (9722 bytes)
7: ==Converters: status and summary table==
103: ...L and mzXML. Here is a [[Msconvert Capabilities | summary]] of what it can do and can't do in its installat... - TPP Tutorial v1 (43187 bytes)
320: '''In the pepXML viewer, return to the Summary tab and select Sorting by xcorr, change the radio... - Software:Out2Summary (104 bytes)
1: ...t and TurboSequest *.out files into a single HTML-SUMMARY file ready for use with the TPP. - Building Peptide Atlas (26978 bytes)
259: ...ncat.PAidentlist; creates experiment_contribution_summary.out, PPvsDECOY.dat, and out.2tonsequences)
266: ...s_nspec-multobs.gif''' -- experiment contribution summary plot
267: * '''analysis.out''' -- a summary of the results, plus instructions to create an am...
272: ...mary page and creation of experiment contribution summary plot
310: ...emove references to multiply-observed peptides on summary page. Make plot look at all peptides. - TPP Tandem search (19915 bytes)
289: == Summary ==
290: In summary, this tutorial has discuss the steps to perform a... - TPP:4.2.1 Release Notes (3668 bytes)
60: Summary file: - PeptideAtlas software (2240 bytes)
11: ...otXML files to new directories), showProteins.pl (summary of proteins in pepXML). - Msconvert Wine (11104 bytes)
111: ...e. The program readmzXML was then used to dump a summary of the resulting mzML file and the values compare... - TPP Amazon Machine Images (12796 bytes)
181: Summary Text: Official image for the Trans-Proteomic ... - TPP SEWW Demo2012 (29568 bytes)
224: === 9. View the summary information on the run ===
226: ''Summary''
228: * Click on the ''Summary'' button
235: * Close these two windows and the top-level summary window
357: To check the status, click on the ''Summary'' button. The ''Overall status'' will be on the ... - TPP AMZTPP (17851 bytes)
240: ...ng all of its many options. To display the short summary simply run the program without any options or com... - TPP:4.7.0 SVN Log (41695 bytes)
426: ... decoy-based analysis results; added quantitation summary and parameters to 'Run Options' tab.
799: ...Prophet results to link out to the correct search_summary thereby allowing to a link on each spectrum to di... - TPP:4.7.0 Release Notes (9008 bytes)
76: ...Prophet results to link out to the correct search_summary thereby allowing to a link on each spectrum to di...
119: ** Added quantitation summary and parameters to 'Run Options' tab. - TPP:5.0.0 SVN Log (143410 bytes)
1862: ... file: extract mzML filename from pepXML msms_run_summary tag, go back to old behavior if file is not found...
1902: [TPP Models] Capture St.Peter analysis summary values; minor JS code cleanup
2146: ...lters and options; added iProphet quick-filter to summary section; expanded size of filename text box; re-i...
2393: ... tab menu title (mouse-over still displays status summary of all jobs)
2561: ...tProphetModels] Make sure we insert the <analysis_summary> tag set before <dataset_derivation> as per the s... - TPP:5.0.0 Release Notes (17167 bytes)
59: ... tab menu title (mouse-over still displays status summary of all jobs)
95: ** Added iProphet quick-filter to summary section
127: ** Modified unique_search_summary_basename restriction to also include search_engin...
129: ...oved errant search_engine attribute from msms_run_summary (was mistakenly re-added in v118)
253: ** Fix a bug with unclosed analysis_summary tags - TPP:5.1.0 SVN Log (66940 bytes)
133: ... Removed non-compliant id attribute from analysis_summary; added an extra test for <dataset_derivation> tag...
385: ...y open tag is found while inside another msms_run_summary...
450: ...to mzid. 2) if given an mzid file, it is read and summary statistics provided. AND the first instance of a ...
466: iProphet: keep track of open analysis_summary tags and close all open ones, when they are neste...
493: ...elected display options and filters in respective summary texts - TPP:5.1.0 Release Notes (19616 bytes)
164: ...elected display options and filters in respective summary texts
337: ... Removed non-compliant id attribute from analysis_summary
344: ...y open tag is found while inside another msms_run_summary.
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