Chromatography Forum

Thanks in advance.

Simply cannot get the Thermo LTQ ion trap MS tune pass the manufacture's suggestion. No matter what we tries, the peah 524 (MARFA) is only at 30% of the base peak (supposed to be aound 60%). The tube lens voltage seems to be the major factore affecting the relative peak intensity for low (caffeine at 195) and high mass (Ultarmark at 1222, 1322, 1422, etc). If the tube lens voltage is near 100V, 195 is the base peak, near 200V, 1522 is the base peak, either way, peak 524 won't exceed 30% of the base peak.

New tube lens, new detector, new tuning solution. After installing a new electron multipler and restoring the factory calibration, re-calibrating th eystem failed to obtain acceptable mass and resolution calibration after quite a few tries. The service engineer seemed lost, so did I.

Any idea what could be wrong?

Does the auto-calibration fail? If not, you don't have a problem. The relative heights of the caffeine, MRFA and Ultramark peaks shouldn't actually be all that important. The calibration just needs to find enough of each to be satisfied.
As well as tube-lens voltage, the relative heights depend rather strongly on how you made the calibrant! The ultramark is incredibly sticky, and the recipe uses quite a small volume, which means it's easy to add too much if you get a bit too much stuck on the outside of a Hamilton needle. It shouldn't matter, but err on the low side, not the high side.
If the calibration is failing, which ion is it failing to find, or at what stage is the error happening? If your instructions are to tune to caffeine before you start, I recommend you try tuning to MRFA instead.
Is your calibrant fresh? If you leave it at room temperature for a week, the Ultramark goes peculiar and makes a parallel set of ions at a slightly lower mass. This can confuse low-resolution mass calibration.

IMH, thanks for your help.

Does the auto-calibration fail? yes, falied after finishing the EM gain. The signals for ions above 1500 are too weak (increase infusion speed up to 40ul/min). Repeated a few times, no vail. When you tune on MRFA, caffeine becomes the base peak, all other peaks are only up to 30% of the base peak. You have to tune one ion on the Ultramark side to have their peak become significant.

At begining I also though this kind of tune result may not be a big issue. However, when I run a standard (the highest) for a method run on this instrument, no signal at all (mass range 100 to 200m/z, using either tunes with caffeine as the base peak or Ultramark as the base peaks), the backgroud looks wired. The problem emerged right after annual PM. Before PM, same standard had a very nice sharp peak. Unfortunately, we don't have previous tuning record retained.

Is your calibrant fresh? Yes, neat compounds were procured three weeks ago, stock solution two weeks old, tuning solution prepared freshly daily

so it passes EM multiplier gain but then fails when it starts looking for the peaks prior to normal-scan resolution?

Since this happened straight after a PM visit, I would contact Thermo to get it fixed. Also, it's highly likely their engineer did a calibration before he/she started the maintenance to check the state of the instrument, and did another after they'd finished, so it may be that they have a copy of previous values stored away somewhere. The other way to get many of the most useful parameters is to go to an old data-file in QualBrowser, change a window to Report - Status log, and scroll down. It would be very useful to do this with a file that worked, before the PM, and a file that has failed, after the PM, and compare the two!

I don't think it's normal to lose the Ultramark peaks by tuning on MRFA. Some people tune on caffeine, which can be a problem because it's just so small a molecule, but MRFA should be a good compromise giving reasonable efficiency over the whole mass range 100-2000.

If you infuse calibrant and look in the tune window, is it a horribly small signal compared to normal?

Do check all the obvious things: that liquid is actually getting to the spray needle, that the PM engineer didn't leave the spray needle in a really silly position. If you're feeling adventurous, you could vent the instrument and make sure the tube lens and skimmer are actually plugged in... but I'd definitely get the Thermo engineer to tell you why it's not working post-PM!

IMH, thanks again.

The service engineer was on site and was able to get the calibration pass. It seems to be a bug in the software system: when you calibrate the mass in the normal resolution mode, the enhanced resolution is default, which is why the detector cannot find some peaks (outside the endhance range).

However, the MRFA peak is still not good, even both caffiene and Ultramark get desirable sensitivity. The low mass and high mass relative intensity is only affected by one parameter: the tube lens voltage (is that wired?). The service engineer will be back today and we will see what can find out.

I'm really happy you're getting somewhere with this. My experience with Thermo engineers has been very good: they know the instruments inside out, and keep coming back until things are behaving properly. Good luck!

Hello

Because you work with a thermo instrument, I have a question concerning the tuning of a specific analyte. Iwork for a small company which bought a Lcq deca Xp plus years ago. I have manage to set things up and made it to work. The thing now is that the LC Tee Union (part number 00101-18204) is missing. It is use to infuse a pure analyte to the MS using the LC flow.

Is there a way to manage without it? But I guess not because I need a tuning method for every compound I have to analyse.

Thanks