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Waters triple quad resolution vs. calibration file structure

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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The nuances of Waters software and tuning are not my strength. Those that use Waters MassLynx driven LC-MS/MS systems know that there are separate calibration (mass alignment) and resolution (quad settings) tuning files.

The part of the arrangement that I do not understand is the ability to only link a new calibration file to what I call the production source settings files (*.ipr) (I call them that because they contain the optimized method capillary voltage, temperatures, and gas flows, in addition to the MS1 and MS2 quad resolution settings).

When I perform periodic optimization of the resolution and calibration settings and generate these two new files, there is only the ability to link the new calibration file to the source settings file that is in use. Linking a calibration file does not seem to update the MS1/MS2 quad settings. I have to type the most recent quad settings in manually.

If I have several different production source method files in use (different temperatures, gas flows, and capillary voltages) re-linking the newest calibration file is fairly trivial, but manually updating the MS1/MS2 settings in each is slow and error prone.

Am I missing an easy way to do this procedure, so I always have the newest tuning files attached to my production method?
My answer to the question is that I don't know any simpler way to do this automatically in masslynx and there is indeed a risk to make mistakes. I try to label all files with a date to check that .IPR files have dates later than the *.cal. I agree there should have been a more logic way to do it and I think this is changed in waters connect software but I still use masslynx. I keep the pdf with optimized resolution values on the desktop and update all my tune files (*.ipr) manually. The resolution for me have been very stable so have been sufficient to recalibrate with each PM so at least it is not that frequent problem in my case.
I'd agree. You shouldn't need to carry out the calibration and resolution optimisation more than once a year, or when the instrument undergoes very serious maintenance, such as having a quadrupole cleaned or replaced.

It's a bit of a pain updating the values after a change. Since you need multiple .ipr files to cope with different spray-chamber settings (for different chromatographic flow rates etc.), the easiest thing is to update them post massive maintenance, to contain the new resolution settings, and at the same time link them to the latest calibration. But when we had a Xevo TQ-S, we had users who blithely ignored this, and continued to use resolution settings from previous years, with the wrong calibration, and who didn't seem to suffer any enormous drop in sensitivity. The caveat is that we use unit mass resolution mode, in which (as someone pointed out) resolution is terrible. If you're hardly resolving the isotope peaks, then a slight change in resolution, or a drift in calibration by 0.1 amu, won't make any real difference to the number of ions getting through.

Actually the main real practical problem we get is when someone uses a tune file for a new MS method, and suddenly includes a transition in a polarity they haven't previously used, but is unaware that someone modified a gas flow or temperature in one polarity and not the other. Voltages can change instantly. Temperatures and gas flows cannot. So if you have a polarity-switching method, with a tune file with conflicting temperatures and flows between positive and negative mode, you'll get errors as it can't achieve the expected settings.
per_oxid wrote:
My answer to the question is that I don't know any simpler way to do this automatically in masslynx and there is indeed a risk to make mistakes. I try to label all files with a date to check that .IPR files have dates later than the *.cal. I agree there should have been a more logic way to do it and I think this is changed in waters connect software but I still use masslynx. I keep the pdf with optimized resolution values on the desktop and update all my tune files (*.ipr) manually. The resolution for me have been very stable so have been sufficient to recalibrate with each PM so at least it is not that frequent problem in my case.


Thank you! This is essentially what we are doing too. I find it odd that it is possible to link calibration file, but not the resolution file (or just merge them into a single file). I am always finding .IPR files with outdated resolution (MS1/MS2) settings, even if the linked calibration is current.

The other "gotcha" is that value changes entered in to those fields do not persist unless the user presses "Enter" before moving on to the next field. This is unlike most other software. And, of course, saving the file at the end is necessary. Just a lot of moving parts to go wrong.
you are so right!
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