Waters DDA Data Conversion and Centroid Validation in MetaboAnalyst 6.0

MetaboAnalyst
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1

Hello,

I am experiencing an issue preparing Waters LC-MS data for MS1+DDA processing in MetaboAnalyst 6.0.

My data were acquired using a Waters Xevo G2-XS QTof in DDA mode, with five acquisition functions:

  • Function 1: MS1

  • Functions 2–4: DDA-MS2

  • Function 5: LockSpray

Since MetaboAnalyst requires separate MS1 and MS2 files for the integrated MS1+DDA workflow, I have been using ProteoWizard MSConvert to extract Function 1 for MS1 processing, with the intention of preparing Functions 2–4 separately for MS2 analysis.

However, although mzML files containing all five functions were recognized as centroided, the MS1-only files consistently return Centroid = FALSE, even when using vendor peak picking (peakPicking vendor msLevel=1-2) followed by scanEvent 1-1.

The original Waters acquisition method specifies centroid mode, and the resulting mzML files are also labeled as centroided.

Could you advise on the recommended procedure for separating Waters DDA acquisition functions into MS1 and MS2 files compatible with MetaboAnalyst? Is there a specific MSConvert configuration or known limitation that could explain this centroid validation issue?

I would be happy to provide representative RAW and mzML files for troubleshooting.

Thank you for your assistance.

Best regards

2

Hello,

Please share the files with us.

Thanks,

Guangyan

4

Hi Guangyan,

Thank you for your response.

I have uploaded four representative samples to Google Drive for troubleshooting. The files include the original Waters RAW data, the corresponding mzML files containing all acquisition functions, and the MS1-only mzML files generated after extracting Function 1.

You can access the files through the following link: https://drive.google.com/file/d/1HVz_QbxW8dG_d08eqB7gbY0czCu2Vtgw/view?usp=drive_link

Please let me know if you need any additional information.

Thank you for your help!
Natara

5

Thanks for the data. I can confirm they are in centroid form - each MS1 scan holds about 43,000 centroids, most of them low-intensity noise, which is normal for Waters continuum data centroided this way. Yet the centroid check is mainly tuned for our Orbitrap system.

Please try again later. It may take ~48 hours for the public server to update with this fix.

6

Thank you for sharing the data, the server has been updated and you can try again.

I have briefly checked your data files, you might want to increase the intensity filtering option when using MSConvert (i.e. 500 or 1000).

Guangyan