Chromatography Forum

Our lab primarily uses GC/MS, with Agilent 6890/7890 and 5973/5975 (and 5977 soon, if we can fix this damn air leak) mass specs. All EI. I have a fair amount of experience with these systems, but some of our newer analysts do not, and since my experience is mostly trial and error and anecdotal evidence, I'd like some resources on how to better read a tune and how errant results will manifest in sample runs.

This stems from a recent run in which an analyst cleaned the 5975 EI source, ran a tune (which passed the tune eval), and ran a sample batch which subsequently looked terrible (on a new column). I looked at the tune, the 219 and 502 were 220% and 45% respectively, with a horrendous ion focus ramp. To me, this just says the source is dirty and needs to be cleaned again, but I can't articulate as to why this is bad (since it did, technically, PASS).

I'd love some literature or references to materials on how to better read autotunes, lens ramp shape, etc and how errant results will effect samples. For example, if you ion lens looks bad, what is happening to your sample as it passes through. How/why does it effect it in this way?

Sorry if I'm not stating what I'm looking for very clearly.

Pass fail for autotune has quite a wide criteria, but if you use tuning checks such as BFB and DFTPP from the EPA methods you have to pass a much tighter criteria and problems like that will show up much better.

I have analysts here that also only know to run an autotune but have no experience with manually tuning the instruments. Having to manual tune the old 5970/5995 instruments taught me a lot about how the lenses work together. I am not sure if there are any manuals out there to describe how it all works, like you I learned by trial and error.

Mostly I'm looking for good sources on what each piece of the source does as samples pass through them. The two textbooks I have with chapters on mass spec give fairly good info on how ionization works with the filaments and electron stream, but sums of the rest of the mass spec as, 'Then the samples go through some extra lens'. So sort of just hoping for readings on more of a step by step basis. The drawout plate does ______. The ion focus lens does ______.

We use PFTBA as our calibrant, and basically just run autotunes and tune evaluations.

I know how to use manual tuning, but am still a bit in the dark as to how samples are effected by modifying each parameter. Even something as simple as voltage. Things like lens offsets and what not I've never played around with because I don't really know what they do.

Even my knowledge basically comes down to, 'Yeah that looks fine,' or 'No, that's not good, clean it again'.

Each manufacturer does the focusing lenses differently, so there probably isn't a single published work on what they do. There might be some info if you search on the Agilent site, but even there they are pushing things towards the "dumb box" way of doing things. Everyone seems to want to make the instruments so any level of knowledge that a tech has, they can operate the instrument, and if it breaks just call customer service. The operating manual for the 5970 even has board schematics with each resistor and capacitor labeled with its stats and description of what each circuit does so you can trouble shoot them, now they just say "if it doesn't scan call the Customer Engineer".

As for how they work, in EI the ions have positive charges, therefore the repeller will have a strong positive charge to repel the ions, the drawout plate is normally not charged(though I believe on the new High Sensitivity sources they are) and acts as a base to the ionization chamber with a small opening for the beam of ions pushed out by the repeller. Ion Focus and Entrance Lens will pull or push ions depending on their charge and will vary by mass being scanned. Something like Entrance Lens Offset I believe works such that if the Entrance Lens voltage setting is 5v it is actually operating at 5v/amu so 10 amu is 50v and 100amu is 500v(these are just examples) and the Entrance Lens Offset will apply additional base voltage such as 5v so that 10 amu would be 55v and 100 amu would be 505v where if you set the Entrance Lens to 5.5v 10 amu would be 55v and 100 amu would be 550v.

By ramping each lens you see how the settings affect each mass differently, which gives you the nice curves. If the curves all align with each other then setting them at the maximum will give maximum sensitivity, but if they all have different voltages where they peak out, then you can use different voltages to adjust the different ratios of the ions.

To really get the hang of it you have to think in 3D or it seems like 4D looking at how each mass responds to each voltage of each lens and then lens versus lens all to make the ratio come out to what it should be. And with the new systems you can have variable settings for each lens also which throws in another level of adjustments so it is like 5D

There are probably others here that know the systems better than I do and can point out how I over simplified it, but that is a general idea of some of what is going on.

http://www.agilent.com/cs/library/userm ... -90104.pdf

This is a better explanation with nice drawings. Pages 23 and 24 describe what I was trying to above.