Tips for high GNPS hit rate for Waters dataset

[Jason Alcano]

Hello everyone,

I'd like to ask everyone if you have specific working workflows in dealing with Waters dataset for GNPS library search and molecular networking.

What we do is that we use different CEs in Fast DDA mode for the same sample and upload the tandem MS to GNPS. We re-run and get my separate data for MS1 for statistical analysis. We take the .raw file of DDA and convert it to mzML file to upload in GNPS for annotation.

Some told me to use MSE in Waters, but I don't actually know how to deal with that dataset to be able to use in GNPS.

For those who are using Waters QTOF, could you share your data acquisition workflow and how you deal with the data for GNPS upload?

Any comments would be appreciated.

Thank you!