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- Main Page (6445 bytes)
7: ...ence.org/courses/proteomics-informatics-course/ Information and materials from previous courses]
14: ...mats:Overview|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; - Software:Prequips:Inclusion List Builder (3897 bytes)
32: ... protein) identification in BioWorks tabular file format and the Superhirn (MASTER_RUN) file containing th...
58: image:Ilb_basics_03.png|Segment information, inclusion list overview and exported inclusio...
59: ...g|Master table and feature details with mapping information. - TPP:Developer Documentation (23931 bytes)
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...
208: In directory with summary.html and summary.mzXML (as well as the SEQUEST results .tgz or subdirect...
212: In the directory with summary.dat and summary.mzXML, type: - Software:TPP (8915 bytes)
17: ...s.proteomecenter.org/wiki/index.php?title=Formats:mzXML]]
18: ...058 333 425 300 [[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...
90: ===Input Processing: mzXML Tools=== - Software:SpecArray (1001 bytes)
9: ...XML file format and convert them into binary file format - Software:mzStar (1909 bytes)
5: ...ee the [[Software:mzWiff|mzWiff]] page for more information.
9: ...been discovered in the Analyst (ABI/MDS Sciex) to mzXML converter, mzStar. This has resulted in major da...
14: ...lyst (.WIFF) format MS/MS data to [[Formats:mzXML|mzXML]] converter. '''(RETIRED)'''
17: ...BI Q-STAR instrument into [[Formats:mzXML|mzXML]] format. This application is based on a VB
30: ...i/tags/release_3-4-1/trans_proteomic_pipeline/src/mzXML/converters/mzStar/] - TPP:Example data analysis (2562 bytes)
20: ... search results must first be converted to pepXML format for further analysis with the TPP. - Formats:mzXML (9722 bytes)
1: ...m most vendors can be converted to the open mzXML format.
5: ... [http://sashimi.sourceforge.net/schema_revision/ mzXML schema].
8: All known formats and their converters are summarized in the table...
10: ...pectrometer Instrument-Specific Software and File Formats:'''
13: |+ Compatible Mass-Spec instrument-specific file formats - TPP:Mascot and the TPP (957 bytes)
13: ..."MzXML2Search -mgf file.mzXML" (Note that the old mzxml2other is retired)
17: ...at) back to the directory where the original file.mzXML file is.
21: ...he *.dat file so that it has the same name as the mzXML but with the *.dat extension (file.dat). - 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 create.params (4398 bytes)
83: # Whether or not to use binary format for library created
84: binaryFormat = true
99: # Whether to add mzXML file to the datasetName (e.g. to distinguish betw...
100: addMzXMLFileToDatabaseName = false - 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...
129: ...have a folder named ‘tutorial’ which contains mzXML data for 6 LC runs, folders that contain the .out... - 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.
10: ...obid.pl This is the script that takes a your_file.mzXML and returns a your_file.xml which can be analyzed...
12: * README basic information. - Software:da2tpp (2167 bytes)
9: ...S spectra for database search. da2tpp.pl uses the mzXML file created with CompassXport to find scan numbe...
13: 1. Extract data using DataAnalysis into MGF format
15: 2. Create mzXML files directly from the DA export function or usi...
19: 4. Copy or transfer all mzXML files belonging to each MGF file to the same dire...
24: da2tpp.pl (outputformat) (mode) mgffile - Software:RAMP (2074 bytes)
4: ...ats:mzXML|mzXML]] format, as well as handle other formats such as mzData. RAMP itself is C-language code; ...
8: *[[Software:MzXML2Search|MzXML2Search]] – RAMP
28: ... makes RAMP fairly dependent on the whitespace in mzXML, and occasionally the order of attributes within ...
31: *[[Software:JRAP|JRAP]]-- java mzXML parser
32: *[[Software:RAP|RAP]]-- earlier xerces-based mzXML parser, retired. - 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
16: ...strument Acquisition Software !! File Type !! TPP mzXML converter - Software:trapper (1991 bytes)
1: ...er: Agilent MassHunter format (.d directories)-to-mzXML converter'''
5: ...Hunter format (.d directories) to [[Formats:mzXML|mzXML]]. The program relies on the MassHunter Data Accq...
11: ...] project. This tool supports all the same native formats as the previous tools, is better supported, and ...
24: ...viewvc/sashimi/trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/ trapper sourcecode] from the ... - 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.edu.sg/~wongch...
37: ...www.peptideatlas.org/ PeptideAtlas] to retrieve information about PTPs (Proteotypic Peptides). - 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...
19: ...s should be stored in the <experiment> directory. mzXML files should be symlinked (use ln -s) to each <se...
33: # link mzXML files to current directory (like creating shortcu...
34: foreach file ( *.mzXML )
42: /sbeams/bin/tandem/runtandemsearch *.mzXML - Terry's blog (18394 bytes)
10: ... Swiss-Prot entries from different species in XML format; come up with list
92: * incorporate into a program which processes mzXML files and adds a value in the <search_score> fiel...
128: * Incorporate PeptideProphet information (e.g. probabilities) into PeptideAtlas. When c...
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