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- Main Page (6445 bytes)
7: ...ence.org/courses/proteomics-informatics-course/ Information and materials from previous courses]
14: ...erview|SPC 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: ...ll Parser programs (children of Parser.cxx) parse pepXML and protXML with the constrain that all text be e...
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...
251: ===Converters to pepXML=== - TPP:7.0.0 Release Notes (6884 bytes)
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...
66: === [PepXMLViewer.cgi:] === - 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
40: ...inProphet should be used if and only if the input pepXML file(s) were created by iProphet. ''iProphet is n... - Software:TPP (8915 bytes)
17: ...p://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML]]
18: ... [[http://tools.proteomecenter.org/formats/pepXML/pepXML_xmlspy_docs.html]]
19: ...77 333 1168 300 [[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:Example data analysis (2562 bytes)
19: ===== Converting Searched Data to pepXML =====
20: ... search results must first be converted to pepXML format for further analysis with the TPP.
24: ## Click on the '''pepXML''' tab.
25: # In the first pane, ''"File(s) to convert to pepXML"'', click on the ''"Add Files"'' button.[[Image:P...
32: # Click on the '''Convert to PepXML''' button in the fourth pane, ''"Convert!"''. - Formats:pepXML (2274 bytes)
1: ...erters are available to transform output files to pepXML.
3: ==PepXML Schema ==
5: The latest version of the format is version '''1.23'''.
7: ...eforge.net/schema_revision/pepXML/pepXML_v123.xsd pepXML 1.23 Schema] (xsd)
35: ==Search-Engine to pepXML converters== - Software:Mascot2XML (2806 bytes)
5: ...cot search results in .dat files to pepXML (.xml) format.
8: ...2XML''' coverts Mascot-specific search results to pepXML.
13: ..., under the Mascot mode --> Analysis Pipeline --> pepXML
21: ... -html : generate html output (default output is pepXML)
24: -desc : generate protein description in pepXML output - TPP:Mascot and the TPP (957 bytes)
13: ...ur mzXML files of interest to mgf (Mascot generic format) files by "MzXML2Search -mgf file.mzXML" (Note th...
23: * Convert MASCOT search results to pepXML with "Mascot2XML <file.dat> -D<full/path/to/datab... - Software:SpectraST (70083 bytes)
7: ...t predictable manner, the MS/MS spectra contain information that can be used to deduce the peptide sequenc...
47: * Clickable (HTML) search output format
66: ... Importing libraries from X!Hunter and BiblioSpec formats
75: * Binary library format, enabling speed gain
76: * Library information and statistics in preambles of .sptxt and .pep... - Spectrast.params (3605 bytes)
7: # A database file to be included in .pepXML outputs for downstream TPP processing - replace w...
29: # Output file format: pepXML or xml (pepXML format), txt (fixed-width text), or xls (tab-delimited t... - Spectrast create.params (4398 bytes)
9: ### PEPXML ###
83: # Whether or not to use binary format for library created
84: binaryFormat = true
91: ### PEPXML ### - 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:ProbID (2453 bytes)
2: ... identifications and output the results in pepXML format, which subsequently can be analyzed by the [[Soft...
7: ...MS spectra using protein sequence database (FASTA format). This jar file includes both the source code and...
9: * example.dta This is the file format of MS/MS spectra that ProbID takes.
12: * README basic information. - Software:da2tpp (2167 bytes)
5: ...ult files incompatible with the TPP conversion to pepXML. However, DA is a powerful extraction software fo...
13: 1. Extract data using DataAnalysis into MGF format
24: da2tpp.pl (outputformat) (mode) mgffile
26: Outputformat:
27: -mgf Outputformat will be written in MGF format - TPP:Related Tools (6244 bytes)
2: ...ial. Some of these tools provide compatible data formats that can be used as input to the TPP, while othe...
4: ...pectrometer Instrument-Specific Software and File Formats==
10: ...e [[Formats:mzXML]] for an overview of compatible formats and converter software.
14: |+ Compatible Mass-Spec file formats
27: ==Compatible Mass-Spectroscopy Input File Formats== - Software:TIQAM (7374 bytes)
6: ==Detailed information and reference==
10: ...which should be targeted, pepXML files or tables (format: peptide, number) can be uploaded. Peptides are s...
18: TIQAM expects the following data formats:
19: * Centroided [[Formats:mzXML|mzXML]] data (use [http://web.bii.a-star.e...
21: * pepXML files. This file is generated by the [[Software:T... - 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 m...
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... - Terry's blog (18394 bytes)
10: ... Swiss-Prot entries from different species in XML format; come up with list
78: ...ications with probabilities less than this in the pepXML file, even if the ProteinProphet adjusted probabi...
92: ...d adds a value in the <search_score> field to the pepXML. David S. has already expressed some interest in ...
128: * Incorporate PeptideProphet information (e.g. probabilities) into PeptideAtlas. When c...
166: ...se separator that he uses in CometViewer (part of pepXML viewer) - Building Peptide Atlas (26978 bytes)
13: ...art with one or more PeptideProphet output files (pepXML) for each experiment in each project.===
14: ...rmal patients and from two diseased patients. The pepXML files should be created by searching the spectra ...
18: ...ful when referencing files using wildcards if the pepXML files all reside at the same level in the directo...
39: Be sure that the input pepXML files were not already processed by iProphet -- y...
41: The resulting pepXML files will be used to generate final peptide prob...
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