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- Main Page (3358 bytes)
7: ...ence.org/courses/proteomics-informatics-course/ Information and materials from previous courses]
16: ==[[Formats:Overview|SPC open proteomics data formats]]: mzXML, pepXML, protXML==
17: ...rmats:protXML|protXML]] on the [[Formats:Overview|Formats]] page.
25: * conversion of raw data to open formats;
27: ... conversion of search engine results to a unified format; - Software:Prequips:Inclusion List Builder (3897 bytes)
9: === Overview ===
32: ... protein) identification in BioWorks tabular file format and the Superhirn (MASTER_RUN) file containing th...
58: ...basics_03.png|Segment information, inclusion list overview and exported inclusion list.
59: ...g|Master table and feature details with mapping information. - TPP:Developer Documentation (23931 bytes)
195: ===Overview===
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, ... - Software:TPP (8928 bytes)
4: == Overview ==
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: ...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... - Formats:mzXML (9722 bytes)
1: ...m most vendors can be converted to the open mzXML format.
5: ...rsion. The offical XML Schema components for the format are available at [http://sashimi.sourceforge.net/...
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 - Software:ProbID (2453 bytes)
1: ==Overview==
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. - 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)
2: ...ection, transition generation and validation. The overview of the software supporting work flow is illustrat...
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... - TPP Tandem search (19915 bytes)
22: ...''The mass spectrometer data is provided in mzXML format and can be downloaded via'''
25: ...ftware like TPP. Various proprietary and raw file format from mass spectrometer vendors can be converted t...
30: Information on installing and downloading the Windows dist...
75: ...proteomics pipeline GUI. The Home tab contains information about TPP and the structure of the GUI, along ...
81: ...ipeline. The first tab is Home, which contains information about the TPP. The second and third tab is use... - NewFrontPage (4627 bytes)
24: [[Software:Overview| SPC Software Overview]] page lists (almost) all of the open-source soft...
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:4.5.0 SVN Log (242349 bytes)
190: ... when pressing 'Enter' to switch directory; minor formatting fix to PepC page
383: Fixed page format to fit page width, got rid of wasted space;
386: Code clean-up: took out unused code, re-tabbed/formatted.
1090: ...c_pipeline/extern/ProteoWizard/pwiz/doc/technical/formats
1091: ...c_pipeline/extern/ProteoWizard/pwiz/doc/technical/formats/index.html - TPP Tutorial (17174 bytes)
3: == Trans-Proteomic Pipeline Overview ==
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... - TPP AMI 4.7.0 README (3773 bytes)
3: ==== Overview ====
22: ...ww.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27121 MyriMatch] - Highly accurate tandem ...
39: ...t utilities on manipulating alignments in the SAM format.
59: * [http://www.bioinformatics.babraham.ac.uk/projects/fastqc FastQC] - quali...
100: ...interface, petunia, was modified to include EC2 information when checking for newer versions of TPP on ses... - TPP AMI 4.7.1 README (3529 bytes)
3: ==== Overview ====
22: ...ww.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27121 MyriMatch] - Highly accurate tandem ...
39: ...t utilities on manipulating alignments in the SAM format.
59: * [http://www.bioinformatics.babraham.ac.uk/projects/fastqc FastQC] - quali... - TPP AMI 4.8.0 README (3528 bytes)
3: ==== Overview ====
22: ...ww.mc.vanderbilt.edu/root/vumc.php?site=msrc/bioinformatics&doc=27121 MyriMatch] - Highly accurate tandem ...
39: ...t utilities on manipulating alignments in the SAM format.
59: * [http://www.bioinformatics.babraham.ac.uk/projects/fastqc FastQC] - quali... - TPP:5.0.0 Release Notes (17167 bytes)
9: == Major Changes and Overview ==
63: **** Fix formatting of message when no jobs are present
112: ** Added ability to format unruly values into decimal or scientific notation
151: ** Updated and reformatted usage statement
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