Extracting raw data from Agilent MassHunter or .mzdata.xml

[ParsingProblem]

Hello, I am not a biochemist, but I am working with one to collect statistical information about liquid chromatogram data. We are attempting to extract the raw data from Agilent MassHunter runs. I have read through some of the posts here and elsewhere about chromatography results formatting and it sounds as though .mzdata is the most accessible.

I have tried to find information about how to interpret the symbols in the mzdata.xml files produced from our MassHunter data, but have not found anything with enough direction or context to successfully extract the data.

We are trying to find three series of data:

Time
Intensity
Mass/Charge Ratio

This data must be written to file somewhere, but I can't seem to find a good way to decode the binary array data compression.

Is this doable? Has anyone here done this before?

Thank you for any thoughts on the matter.

[ParsingProblem]

I was able to find a tool from the ProteomeCommons to decode the mzdata.xml file after a great deal of searching and accepting Protein-based results instead of focusing specifically on procedures applicable for Lipids.

http://www.proteomecommons.org/current/531/

We are getting text files that look almost right, but the numbers are "noisy" and inconsistent seeming. Has anyone used this software before? If details about the structure of our text files are helpful, I can post them.

Thank you

[lmh]

you could have a look at xcms too; it might have some useful features depending on what you are trying to do. It's a product of the Scripps institute (search for xcms, Scripps or metlin).