Posted by: Edlira Nano
Date: 2010-11-10 15:03
Summary: New XML MassChroQ input schema, new features.
Project: MassChroQ

• Development Status : 5 - Production/Stable
• Environment : Console (Text Based) : Win32 (MS Windows) : X11 Applications
• Intended Audience : Developers : End Users/Desktop
• License : GNU General Public License (GPL)
• Natural Language : English : French
• Operating System : Windows : GNU/Linux
• Programming Language : C++
• Topic : Bio-Informatics : Medical Science Apps.

Content:

The schema of the XML input file to MassChroQ has been competely redone in a more intuitive way and in order to offer more possibilities. More precisely  : 

- It is now possible to define several alignment methods and launch different alignments on different groups.

- Until now, the reference msrun for the alignment of the group was automatically the first msrun in the definition of the group. Now it is possible to choose it in a new attribute \"reference_msrun_id\" of the \"align\" tag.

- One can now define different quantification methods. A quantification method contains a xic_extraction method, a xic type, xic filters and a peak detection method. This way,  MassChroQ can quantify different groups with different quantification methods.

- The different output files and formats for the quantification results have been revidited. The tsv (tabulated separated values) format and the xhtmltable formats will both produce two files : one with \"_pep\" suffix containing the results ot the peptides quantification, and one with \"_prot\" suffix for the proteins quantification.

- New feature : the xic traces one wants to produce during quantification have been revisited in a more flexible and rich way. Three possible sorts of xic traces : all the xics are traced (\"all_xics_traces\" tag);  a given list of peptides is traced; a given list of mz and a given list of mzrt values. 

A generic complete XML input file illustrating these possibilities can be found in Docs ( https://sourcesup.renater.fr/docman/?group_id=797).