Original submission:

This document defines an XML schema that can be used to describe the outputs of quantification software for proteomics (quantitative values about peptides and proteins) and potentially metabolomics (quantitative values about small molecules), derived from analysis of mass spectrometry data.

All example files can be downloaded manually from:

http://code.google.com/p/mzquantml/source/browse/#svn%2Ftrunk%2Fexamples%2Fversion1.0-rc1

http://code.google.com/p/mzquantml/source/browse/#svn%2Ftrunk%2Fexamples%2Fversion1.0-rc1%2FABRF

http://code.google.com/p/mzquantml/source/browse/#svn%2Ftrunk%2Fexamples%2Fversion1.0-rc1%2FCPTAC

The format SHOULD support the following specific techniques used in proteomics (see section 5.3 of the specification document for examples of their encoding):

• MS1 label-free intensity
• MS1 label-based e.g. SILAC and metabolic labelling such as ¹⁵N
• MS2 tag-based e.g. iTRAQ / TMT
• MS2 spectral counting

We expect that the format MAY also be able to cover the following techniques adequately, although these have not been tested in great detail at this stage, and we encourage further input from users of these techniques:

• Quantification by selected reaction monitoring (SRM)
• Absolute quantification based on averaging the intensities of features e.g. Waters Hi3 technique
• Small molecule quantification (in metabolomics)
• MS2 intensity-based approaches
• MS2 label-based approaches