Matching QTOF and Orbitrap datasets (via setting up a custom database?)

August 31, 2023, 04:05:13 AM

Apologies for perhaps a primitive question, but I’d like to ask advice about how to optimally proceed with the following task:

We have an Orbitrap dataset and an QTOF dataset, generated from partially overlapping sample sets, using ~same LC instrument.
We need to match the molecular features in these datasets (I mean, find what feature corresponds to a QTOF compound in the Orbitrap dataset).

I’m thinking this could be accomplished by setting up a custom metabolite database from one of the datasets, and use that to annotate the other dataset in MSDIAL.
If you agree, could you please point us to a tutorial about converting our dataset to a database for this purpose?
If you have better suggestions for a protocol, please let us know.

As a side note, the QTOF dataset has files for 10-20-40 kV. Apparently 10 kV would be best match for Orbitrap (because of the fragmentation power). But 20 kV and 40 kV would provide additional fragmentation info. Is it possible to somehow more or less merge these to utilize all available data for the matched compounds, after we have completed that?

With best regards,
Mikael Niku