MRM / isotopologue support, coming from El-MAVEN context
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I have a list of MRMs peaks in whose traces I want to integrate peaks. The software often doesn't match up all the MZML MRMs to the correct entry in the compound list I load, so what it calls the SRM list often contains mismatches. My initial workflow consists of the following:
- Relink misassigned MRMs;
- Manually correct the integration windows;
- Manually change the thresholding settings where warranted for background exclusion.
El-MAVEN allows me to edit bookmarks once placed into the table. Is this possible in MAVEN, just through a click sequence that I'm not picking up? I'm not quite getting how to manually adjust integration windows after holding Shift and dragging.
No, it isn't possible to modify bookmark information through the GUI after the bookmark has been made, but you can re-bookmark a bookmarked peak, or re-bookmark the same peak once again. I've found that in practice, the same peak ends up getting bookmarked several times before everything looks good. You can always delete peak groups you don't want to retain using the 'Delete Group' button
whether MAVEN has any feature that allows me to batch apply the integration window and threshold setting to several MRMs that monitor different isotopologues of the same compound. If present, such a functionality would save quite a bit of time. This is not a feature in El-MAVEN as far as I'm aware.
A good amount of functionality has been built out for MRM work and isotopologue work. However, we (at Calico) typically do our isotopologue work on MS/MS data, and our MRM work on a Sciex 7500, and we haven't tried a combined workflow. Some of the MRM stuff is very heavily geared towards the Sciex 7500, so it might not work if you've got a different instrument. The only way right now to combine MRM data with isotopologue work in MAVEN would be set up you transition list to extract various individual isotopes in the envelope, and organizing isotopes into their appropriate envelopes downstream.
Is it more expedient to use the peak autodetection feature with carefully applied settings? I have done so when processing Q-ToF MS data, but that's a different context from targeted MS/MS runs.
Yes, I would recommend using the autodetection feature. If you do, you will need to make sure the
SRM/MRM Searchcheckbox is checked:
A few bugs that were identified during live coding section:
RT lock not working for SRM data
Peaks search not working for SRM data (6500+)
If there are multiple entries with identical Q1/Q3 values and no parsed name, the QQQ mapping chooses one of the two compounds. It would be nice to be able to manually update the compound linking to SRM data (e.g.-> oxaloacetate / pyruvate).
Will wait on QQQ + SRM stuff, happy to re-prioritize if active interest in this area.