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- Main Page (6445 bytes)
7: ...ence.org/courses/proteomics-informatics-course/ Information and materials from previous courses]
14: ...PC open proteomics data formats]]: mzXML, pepXML, protXML==
15: ...rmats:protXML|protXML]] on the [[Formats:Overview|Formats]] page.
22: * conversion of raw data to open formats;
24: ... conversion of search engine results to a unified format; - TPP:Developer Documentation (23931 bytes)
33: ...rograms (children of Parser.cxx) parse pepXML and protXML with the constrain that all text be enclosed with...
199: ====Conversion of raw spectroscopy data to mzXML format====
203: ====Converting search engine results to pepXML format====
204: Analysis programs begin with a pepXML-format file called 'summary.xml', containing the peptide...
260: Converts summary.html to summary.xml in pepXML format. Uses sequest.params file in current directory, ... - TPP:7.0.0 Release Notes (6884 bytes)
15: * Updated protXML schema to v10
25: ... MZP_MZ5), which will include support for all HDF formats (MZ5 and mzMLb). Note that mzMLb.gz is not yet s...
27: ...read in the entire spectrum even if only header information is requested. This is because it wouldn't be p...
39: ..., to allow the new iProphet NSM model using ptm information content to use all results in the file in an u...
47: * NSM model now weighs the evidence by ptm information content, significant speed-boost for NSP model... - Software:ProteinProphet (6941 bytes)
8: ...is present in the sample. This protein grouping information is then employed to adjust the individual pept...
30: ... all input interact datasets with mz/XML raw data format)
31: ... DELUDE: do NOT use peptide degeneracy information when assessing proteins
52: Proteins are clustered into groups within the protXML element <protein group>. Usually there is just on...
58: ...independent evidence to earn its own entry in the protXML file." - Software:TPP (8915 bytes)
17: ...p://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML]]
18: ...058 333 425 300 [[http://tools.proteomecenter.org/formats/pepXML/pepXML_xmlspy_docs.html]]
19: ...[[http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html]]
42: ...ion guides, which are more detailed and contain information specific to certain distributions: [[Linux Ins...
95: [[Software:mzStar|mzStar]]: SCIEX/ABI Analyst format to mzXML converter - TPP Tutorial v1 (43187 bytes)
15: ...ation of TPP and only briefly touches on the bioinformatics behind the tools which are included in TPP.
23: ...ecific format and one instrument independent data format will require more than twice as much storage spac...
27: ...mall ''Itallics'' is use for notes that contain information that is not required to complete this tutorial...
35: Information on installing and downloading the Windows dist...
131: ... search results and convert the raw data to mzXML format. These steps are covered in the last section - B... - Software:SuperHirn (11737 bytes)
11: * parsing of protXML data updating MS/MS ids with ProteinProphet proba...
73: 1.) copy the parameter in this format to your param.def file:
121: ...data || If MS1 data is in centroid (1) or raw (0) format || 0 || - - Expert search and TPP usage (12929 bytes)
15: ...name of the person who generated the data, in the format used in SBEAMS. If that investigator is not regis...
22: Paths are hardcoded within pepXML and protXML files. If you move these files, you must run the ...
152: ...plain FASTA files, but rather FASTA files must be formatted with something like:
153: /package/genome/bin/formatdb -i YeastCombNR_20070207_ForwDecoy.fasta -p T -o... - Building Peptide Atlas (26978 bytes)
52: ProtXML inherits protIDs from biosequence set.
71: ...of the TPP, adjusts pepXML probabilities based on protXML info, gathers all PSMs (peptide-spectrum matches)...
77: ...ept for the sorting of the lines. They are in tsv format and have the following fields:
89: # nsp adjusted probability from protXML
90: # n_adj_obs from protXML - NewFrontPage (4627 bytes)
26: **For information about the (sometimes confusing!) relationship ...
27: ...mats:protXML|protXML]], on the [[Formats:Overview|Formats]] page.
38: ...ful information about the [[Formats:mzXML|mzXML]] format.
50: ...rs MediaWiki user's guide] for an introduction to formatting and editing pages. - TPP Tutorial v2 (15736 bytes)
19: ...the vendor's raw data format to the open ''mzML'' format, you will need to install the free [http://sjsupp...
30: == 3. Convert raw data to the mzML format ==
32: ...re first convert the proprietary raw data to this format, called '''mzML'''.
57: :''For more information, please go to [http://www.thegpm.org/TANDEM/ap...
63: ...at for downstream processing. This is the PepXML format, and can the conversion can be effected via the '... - TPP:4.4.0 Release Notes (31941 bytes)
12: ... project. This tool supports all the same native formats as the previous tools, is better supported, and ...
49: * Minor form closing changes to avoid mis-formatting in IE
71: === protxml2html (ProteinProphet viewer) ===
183: ...UW Heinecke lab (paper has been submitted to Bioinformatics). Changes for integration with Petunia will c...
267: ...l part of which is copied here with total loss of formatting: - TPP:4.6.0 Release Notes (4524 bytes)
14: * Support for ''.mz5'' format
32: * Added column in excel ouput of ''protXML viewer'' that indicates if peptide ion is used as... - TPP Tutorial (17174 bytes)
33: ...the vendor's raw data format to the open ''mzML'' format, you will need to have chosen to install the msco...
44: == 3. Convert raw data to the mzML format ==
46: ...re first convert the proprietary raw data to this format, called '''mzML'''.
71: :''For more information, please go to [http://www.thegpm.org/TANDEM/ap...
163: ...er.org/wiki/index.php?title=Image:Protxml.JPG IMG:Protxml] - TPP:4.7.0 SVN Log (41695 bytes)
76: ...y friendly 'spectrum' link when no matched ions information is available from pepXML
80: ...cores, and add filter options. Also some minor reformatting of filters for PeptideProphet and OMSSA
139: [ProtXMLViewer] Intial commit (alpha) of new protXML viewer. It is *much* faster, uses an index to re...
305: Usage statement formatting. Improved colors and different scale in Heat...
320: in C11. So we renamed it TIME_UTC_. For more information see: - TPP:4.8.0 SVN Log (42174 bytes)
21: [ProtXMLViewer] Added NSP bin link (goes to models page, w...
25: ...atio pvalue] Write pvalue raw data and model into protXML (using a tmp file) so other tools can display/viz...
63: [ProtXMLViewer]
230: * Point to new ProtXMLViewer as default; leave link to legacy viewer;
280: Simplified how version/build information is managed in TPP. Also - TPP:5.0.0 SVN Log (143410 bytes)
386: version *and* build information.
1127: * Changed TPP Information to TPP Support in the start menu drop down men...
1141: TPP-5 : Fixed ProtXMLViewer/old viewer
1147: TPP-5: added back xsltproc (win32) for protxml viewers
1322: TPP-5: Fixing path to url transformation - TPP:5.0.0 Release Notes (17167 bytes)
33: ... Generate error vs min_prob table and insert into protXML (similar to the one produced by PeptideProphet)
63: **** Fix formatting of message when no jobs are present
112: ** Added ability to format unruly values into decimal or scientific notation
117: ** Display new error table from protXML, if present
121: * New versions of ''pepXML'' and ''protXML'' schemae - TPP:5.1.0 SVN Log (66940 bytes)
16: [ProtXMLViewer]
51: - fix text/excel export of loop xlink peptides, Format is as:
79: - Some code formatting for consistency
100: ...as no peaks (instead of segfault). Also: code re-formatting!
254: [ProtXMLViewer] Display and export protein length - TPP:5.1.0 Release Notes (19616 bytes)
14: ** Linked from ''ProtXMLViewer'', but can be used stand-alone
21: ** Linked from ''PepXMLViewer'' and ''ProtXMLViewer''
78: * ''ProtXMLViewer''
81: ...isplay and export protein length, when present in protXML
89: ** DIAUmpire support improved with native format reading
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