In the ProteomeXchange (PX) consortium there are currently three kinds of proteomics data resources:
Published (archival) resources contain processed data as published by the authors. PRIDE is representative of this type of data in the consortium for tandem mass spectrometry (MS/MS) datasets. The PASSEL component of PeptideAtlas is representative for selected reaction monitoring (SRM) datasets (Figure 1).
Figure 1. Basic workflow for MS/MS data in ProteomeXchange.
Raw resources contain potentially very large, raw data files and other accompanying files. There are currently repositories for these kinds of files at EMBL-EBI for (MS/MS) datasets. SRM datasets are stored at the Institute of Systems Biology (ISB; Figure 1).
Reprocessed (secondary data) resources build on the primary data provided by submitters and are stored in archival resources. PeptideAtlas and UniProt are examples of secondary data resources that are members of the PX consortium (Figure 1).
After submission to an archival resource such as PRIDE, files are propagated to the appropriate archive and secondary data resource, from where they are made available to users (Figure 1).