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. 2011 Jun 19;10(10):M111.008334. doi: 10.1074/mcp.M111.008334

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© 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

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Fig. 3. — ABRF sPRG2010 experiment: MIAPE and PRIDE XML creation pipeline. Step 1) Both peaklists (peaklistA.mgf and peaklistB.mgf) derived from the two experimental approaches (CID and ETD fragmentation modes) are submitted to Mascot. The final results provided by the search engine are exported using mzIdentML format (identificationA.mzid and identificationB.mzid). Step 2) Automatic generation of MIAPE documents: the source peaklist and resulting mzIdentML identification file (i.e. peaklist A.mgf in addition to identificationA.mzid) are submitted to the ProteoRed MIAPE web toolkit (PMWTK) to create the corresponding MIAPE reports (MIAPE MS from the MS peak lists and MIAPE MSI from the mzIdentML). Step 3) Export to PRIDE XML from MIAPE MS and MSI. Finally two PRIDE XML documents (CID and ETD modes) are generated and were submitted to the central repository (http://www.ebi.ac.uk/pride) for public access.