Previous | Next | See Also

This document gives a brief introduction into how quantitative proteomics data is stored in PRIDE XML files.

Quantitative data in PRIDE XML

When the PRIDE XML format was developed quantitative methods for MS based proteomics experiments were not widely used. Therefore, the PRIDE XML format does not inherently support the storage of quantitative results. Using a feature present in PRIDE XML that allows one to store additional data for proteins and peptides we defined away that enables us to nevertheless store simple quantitative results in PRIDE XML files.

New methods to quantify proteins in MS based proteomics are constantly being developed. Therefore, it is very difficult to define a common way to represent this heterogeneous data. The PRIDE database is focused on storing proteomics data that is part of a manuscript or publication. Therefore, we decided to build the support for quantitative data in PRIDE XML files around the requirements for this specific task.

Supported quantitative data

PRIDE XML only supports the storage of final quantitative results but not any intermediate results generated during the processing of the raw data. For every protein and peptide one single value can be stored per multiplexed sample (if applicable). In a 4-plex iTRAQ experiment, for example, it is thus possible to report one value per reporter ion per peptide and protein. This thus results in 4 quantification values per protein and peptide.

The stored quantitative values can either be the final calculated ratios (with the quantitative value for the reference sample set to 1) or the raw measured reporter ion intensities. This primarily depends on which of these numbers are considered "final" by the submitter.

See Also

Other topics which will help you understand the data you are exporting: