I am assuming you are working with a 5977x (SQ) system and not a 7000x (TQ) system.
Agilent has specifications around the m/z 69-219 ratio on 597x systems in autotune but the range is quite large and there are many variables that contribute to the variation in m/z219 response. One of the major contributors to the response is the source cleanliness. I have found many people don't pay a lot of attention to cleaning the entrance lens but it could be any part of the source.
"atune" tunes the "extractor source" just like it was a standard "inert" source and sets the extractor lens to the same voltage as the source body (traditionally 0V relative to ground).
"etune" tune uses the power of the "extractor lens" to get more ions out of the ionization chamber and down into the quadrupole.
The extractor sources when autotuned with "etune", do normally give a higher mid mass abundance (m/z219 and m/z264). Some people confuse this as lower high mass sensitivity but in actual fact the mid masses are extracted from the source exceptionally well in "etune" and the higher masses also extract more efficiently then "atune" but just not as well as the mid mass. When you are just looking at the normalized spectrum it is hard to compare and sometimes it looks like you have lost some high mass abundance but this is normally not the case. We call this effect a "spectral tilt".
While a system that is tuned with "etune" commonly gives m/z219 > m/z69 relative abundance this is not always the case. Using "atune" m/z 219 it is more often < m/z69 relative abundance.
Library matching only effected slightly but the spectral tilt of the spectrum. Library match scores are heavily calculated based on the presents/absence of an ion and not so much on the relative abundance so using etune gives you the best sensitivity and shouldn't effect your library matching very much.
You may need to update the ion ratios in your quant data base if you are using a quant package (MassHunter Quant or MSDChemstation) but this is a relatively simple change to a quant method.
Direct answers to your questions:
Q. How necessary would it be for the 219 to be higher than the 69?
A. Not very necessary. It depends on the tune algorithm used. I don't like to see m/z219<50% of the m/z 69 abundance but his depends on the tune type.
Q. Would this have a big effect on performance?
A. Generally spectral tilt does not effect "performance" a lot unless it is extreme.
Q. What could be the reasoning for the different 219 values on each source?
A. Many factors. Source cleanliness, source tolerances (how it is put back together), column flow rates, filament alignment, quadrupole transmission, etc
Q. Why am I struggling to achieve this on most of the sources?
A. Depends on the tune type (atune or etune) but I do not normally consider this as a pass/fail criteria.
Some follow up questions are:
1. What tune algorithm are you using? etune or atune? (stune and other algorithms have fix abundance ratios and generally de-optimize the source to achieve these ratios)
2. What is your source cleaning technique?
3. What are the m/z69 to m/z219 ratios you are commonly seeing?
I hope this helps.
Yes it was the 5977 just used for quantitation on etune.
The GC was blanked off as I was cleaning and testing about 15 sources.
I'm thinking it was as I'd used Autosol for the abrasive.
219 to 69 probably high 80's.
Thanks for the incredibly thorough response!
No problems. The systems will tune differently and give different ratios when there is no GC column flow going into the source. I generally recommend tuning a systems with the flow rate you are going to your application. Constant GC column flow is Agilent's recommendation for Agilent GC/MS systems.
I went ahead and flagged the “Correct Answer” on this post. If you still need help though, please let us know and we would be happy to continue working with you.