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MZIdentML is an emerging standard in the proteomic community. Docs. The schema Is shown here.

The program idconvert which is part of the ProteoWizard suite is capable of converting a number of different formats into mzIdentml. When doing the conversion it is useful to have all of the source files available to the converter because the converter is smart enough to find multiple sources and to weave the data into a single document. In particular the combination of prot.xml and pep.xml is supported. If you use this combination it is a good idea to have the original sources used for the search available and in the same spots that they were used in the search because the pep.xml file will not contain the original spectra but only a reference to the file from which they were read.

I have made a few minor changes to the idconvert program to cause it to work properly with pep.xml files and am waiting to see if they are adopted by the main proteo wizard team.

The command line

idconvert --mzIdentML <pepxmlfile> for example MyDirectory>idconvert --mzIdentML interact.prot.xml Will convert the prot.xml file along with any corresponding pep.xml files that are found into a file whose name will be the name of the prot.xml file with .mzid appended. NOTE in the command line the case of the command --mzIdentML is important and failure to follow case exactly will cause the command not to work.

A version compiled for Windows (64 Bit I think) is available in /regis/users/slewis/bin.

Any files generated may be validated using the on line validator.

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