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It seems like it could be possible since fragmentation is reliant on bond energies and the breaking of those bonds. Maybe a M+NH4 has some different energetic interactions than an M+H, causing fragmentation to be a little different? I know this post is older, what did you figure out?
I don’t know of any, but would be interested in learning more about it if someone else knows of any!
We have a nitrogen generator feeding our LC-orbitrap and do not supplement with anything else. It went down recently, and I temporarily had to switch to a dewar and saw no difference in data quality. For reference, our generator produces 99-99.99% purity.
That’s helpful! I am getting the “DIA only” flag on ddMS2 data which is perplexing, but your explanation for “DDA for other ion” is super helpful. Thanks!
Could it be column temperature related? Could the column heater/preheater be malfunctioning and not giving consistent temps and therefore causing systematic RT shifts with changes in ambient temps?
That’s really helpful to know. We typically track the ambient temp measured by the Orbitrap itself (see screen grab below) and are trying to make some building modifications to get this temp below 25-27 C (as consistently as possible). Our all time low is 27.2 with 3 high powered fans and a split AC unit directing airflow- and that’s a recent improvement from where it was sitting at a cozy 30 C. Knowing this now, we’ll continue working on those building mods! Thanks for sharing!
Shoot, it should be in that dropdown menu. Unless you can export as that NIST MSP option and open that in mzVault, I don’t think my workaround will work :/
I think I know of a long way to do this by building a mzVault library in CD of the features you want (I usually mark them with the colored “tags” on the far left hand side). Once you have all your features in the Compounds Table, right click and “build mzVault library”. Then go to the Lists and Libraries Manager, find your new mzVault library in the Spectral Libraries tab, and export it. Then open up mzVault and load your new database file and export from there into excel. That will give you (in a big table that needs reformatting to get to the desired format mentioned in the OP) precursor m/z and fragment m/z with “target” ratios, but in this case since it’s experimental data you used to make the library, it’s observed target ratios.
