Building chromatograms from .mzdata file

[Sydney Dautel]

Hello all,

I frequently use MZmine and really have appreciated the new functionalities in the last version of the software. For the last year I have been using the software on full scan experiments with .raw files and have had no issues. The last few days I have an encountered an issue and would really appreciate some guidance on the subject.

I am currently trying to align data from an MRM experiment collected on an Agilent triple quadrupole instrument. From these experiments I get .d files which I can convert to .mzdata files.  I can import this raw data into MZmine successfully and generate mass lists using mass detection (shown below--the data is correct as compared to the raw file)

However when I try to build a chromatogram with the settings shown below (we can use 1e1 as the minimum height because our noise level is very low with the MRM experiment) the software fails.

It is not able to create a peak list table (shown below).

Do you have an idea of what the issue might be? How might I fix this?

I have included the a copy of the log text as an attachment.

Thanks so much,

Sydney Dautel

[Tomas Pluskal]

Hi Sydney,

The Chromatogram Builder module needs MS1 (full scan) data. It won't work with MRM data.

You can try the MS/MS Peaklist Builder instead, although it will not produce chromatograms, just a single peaklist entry for each MS2 scan.

MZmine does not really have any method to deal with MRM data beyond that.

Best,

Tomas

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[Sydney Dautel]

Thanks for your help.

Sydney

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