Data format conversion: mzXML to mzData

[Judson Hervey]

Hello all--

I have a basic question regarding data file format conversion. My eventual goal is to search data using MyriMatch which-- according to the JPR publication-- accepts MS/MS data in the mzData format.

Is there a straightforward method (eg. program or script) to convert mzXML data to mzData? ... or does MyriMatch also accept mzXML as an input format in addition to mzData?

I'm acquiring data on a QSTAR Elite using AnalystQS 2.0 and converting to mzXML using mzWiff.exe from the TPP. After performing this conversion step, I'd like to be able to convert to mzData (if necessary) and search MS/MS spectra with MyriMatch.

I performed a short search of the web and was not able to find any information if the mzXML > mzData conversion step is even possible (or necessary).

Finally, we were excited with the announcement that Matrix Science has written their own data conversion libraries for *.wiff files (which will soon be available in version 2.4 of the Distiller Toolbox, I believe)... Though it's way early in the game, it would be great to be able to call these libraries in the mzWiff.exe program on a 64-bit machine rather than being stuck in WinXP SP2....

Thank you in advance for your time!

Sincerely,
Judson Hervey

[Matthew Chambers]

MyriMatch has been updated a lot since the initial publication. It doesn't even support mzData
anymore because ProteoWizard doesn't which is what MM uses for I/O. On the other hand, it now
supports all the formats that pwiz does, including the vendor formats on Windows. The recommended
format is mzML. With the next MM update, MZ5 will be a recommended format as well since it'll be
much faster without any metadata loss.

Hope this helps,
-Matt

P.S. Can you link to the announcement about Matrix's "own data conversion libraries"?