Appendix 1: Formats supported by PRIDE for PX MS/MS submissions



a) as raw data

 Formats supported:

  •  mzML, mzXML, mzData. These files must not be heavily processed to be considered ‘raw’.
  • Thermo .RAW, ABSCIEX .wiff, .wiff.scan, Agilent .d/, Waters .raw/
  • imzML, Shimadzu .run/, Bruker .baf, .yep
All peak lists formats (mgf, dta, ms2, pkl) can be supported but they will not be considered raw data. They will be considered as ‘peak list processed files’ or simply ‘peak’.



b) as processed identification results’

Different search engine output files need to be converted to PRIDE XML using existing tools like PRIDE Converter 2 ( Formats supported:

  • Tandem XML
  • OMSSA .csv.
  • Mascot .dat
  • Sequest Crux .txt
  • SpectraST .xls
  • ProteomeDiscoverer .msf files.
  • All accompanying peak lists formats.



c) as search engine output files

Only those data formats that cannot be converted to PRIDE XML are considered to be ‘unsupported formats’ and can use this alternative approach (datasets type B, Datasets containing raw data and search engine output files). At present, there are no reliable converters to PRIDE XML for the following formats:

  • pepXML, protXML.
  • Scaffold format.
  • MaxQuant output files, DTASelect, and many others.
  • mzIdentML files.



d) as others

Other types of files are optional and can be supported as part of a PX submission together with the other files. It is the case of quantitation results (mzQuantML, mzTab), images, etc.