Software:TIQAM
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| - | ==APML== | + | ==Getting Software and Documentation== |
| + | ===APML documentation for MS1 data format=== | ||
| APML is currently used as a standard interface for Corra framework and software developed by Mi-Youn Brusniak at ISB Ruedi Aebersold Lab. | APML is currently used as a standard interface for Corra framework and software developed by Mi-Youn Brusniak at ISB Ruedi Aebersold Lab. | ||
Revision as of 17:56, 6 August 2008
Contents |
Introduction
Corra is a single, user-friendly, informatic framework, that is simple to use and fully customizable, for the enabling of LC-MS-based quantitative proteomic workflows of any size, able to guide the user seamlessly from MS data generation, through data processing, visualization, and statistical analysis steps, to the identification of differentially abundant or expressed candidate features for prioritized targeted identification by subsequent MS/MS.
A goal of Corra was to enable the integration of multiple and disparate LC-MS data analysis tools, and integrate them, seamlessly, with common statistical packages to allow for better comparison between differently-processed datasets, via the addition of statistical measures of confidence and error rates. The integration of tools was achieve via AMPL (Annotated Putative peptide Markup Language) and the various parsers, and in the current build of Corra, we have implemented SpecArray and SuperHirn. Current distributed Corra contains APML adapted open source of SpecArray and SuperHirn.
Getting Software and Documentation
APML documentation for MS1 data format
APML is currently used as a standard interface for Corra framework and software developed by Mi-Youn Brusniak at ISB Ruedi Aebersold Lab.
[View APML Schema] [View APML Schema Documentation]
Installation Instruction
Current distributed Corra v1.5 can be downloaded to your linux system by the following steps.
1. download Corra-v1.5.tgz
2. tar -xzvf Corra-v1.5.tgz
3. The detailed installation and setup information can be found in Corra/doc of the untarred file or by downloading [Corra Installation Guide.doc]
4. example data set The example_mzXML.tgz contains three LC-MS FT runs of wild type yeast and three LC-MS FT runs of gene deletion strain yeast.
Contact Information
Mi-Youn Brusniak, Ph.D. 1441 North 34th St. Seattle, WA 98103 USA mbrusniak@systemsbiology.org
