Chromatography Forum

Hello all,

I wanted to start by saying that recently in the past 2 weeks we have been noticing fluctuation in our signal using ESI+. Basically we used to run an assay with 6 analytes or so + internal standards and have the standard ion abundance values obtained, we then ran these samples and sometimes the instrument performs just fine, then the following day the signal loss is exceptionally, and almost completely lost. Then a few days later on we find these peaks to appear again. It is very inconsistent. But it used to work fine and the method was very consistent up until 2 weeks ago.

The interesting part is that this only happens for MRM mode. When we do a full scan the peaks are always present, but sometimes the MRM does not show up or the the counts are completely lost.

The instrument always always passes the autotune with flying colors, and the 6 polymer peaks are always present with high abundances and the mass axis needs minor adjustment if any.

One question I have is that the autotune tests the mass spec, and adjusts the ion optics and mass axis , but can it ensure that the collision cell is working properly, how would you test if the collision cell is faulty?

Do you all have any ideas what could be causing this?

More recently I have seen on another method that with three consecutive injections of a single analyte and internal standard, the peak ratio between the analyte and internal standard of the same sample fluctuates, sometime the analyte is higher and than the I.S. and then the next injection the analyte is lower, how can this be? If it was an injector issue shouldn't the response be consistently low for each or high for both?

Any ideas of what could be causing these variable instrument responses? Especially since the autotune and checktunes look excellent and have even higher abundances then months ago when the instrument was fine?

This troubleshooting is so frustrating and has taken up so many hours. I have not been able to isolate the problem to the LC or the MS?

FYI, our EMV reading was adjusted to 2100 in the last tune, i know that is high, does anybody have an idea of when this should be replaced? Would an autotune pass if the EMV needed replacing? I was under the impression when the EMV dies the signal goes flat, and there is no way the ions would appear in the autotune.

Our system is an Agilent 1200 / 6400 QQQ

Please provide any input or experiences or suggestions you have.

Thanks so much.

I am not familiar with your MS system, but am familiar with triple quadrupole systems in general and make the following points.

1. Full-scan works fine; Q1 only, or both Q1 and Q3 ?

2. Autotune runs successfully; again, Q1 only or Q1 and Q3 ?

3. EM set at 2100 V---what was setting when new ?

4. Failure to detect selected fragment ions has (at least) three causes, in addition to dying electron multiplier.

(a) failure to fragment parent ions (no gas in Q2; collision energy too low)

(b) if the fragment ions are produced, Q2 fails to transmit them to Q3

(c) fragment ions are transmitted to Q3, which fails (sometimes) to operate correctly in the MRM mode.

Intermittent detectability problems to me suggest issues with power supplies---either a board is failing, or possibly there are loose electrical connections on Q1 and/or Q3.

Please let us know how this issue is resolved.

Well today I decided to perform some maintenance on the MS. I vented the instrument, pulled the source sampling cone and ion transfer capillary, and also thoroughly cleaned the desolvation assembly. I removed the mass analyzer shield and replaced the EMV. I finally put everything back together and am pumping down overnight, tomorrow I will run a full autotune, hopeful this might fix the problem....

I also checked the nebulizer and the spray seems fine, the capillary needle extends very very slightly from the capillary tip.

If not, we will look at the front end LC, make sure the autosampler injection volume is accurate, we will place a small vial and do a series of injections and then see how much volume remains. We will also purge all the lines and go through a solvent rinse and backflush the needle to makesure nothing is trapped.

I am really not sure what the heck is going on, but with a bit of luck, and being hopeful that tomorrow morning she autotunes fine and the assays are working again.

If anybody else has any other suggestions please comment.

Hi guys

the problem was solved, turns out it was an overdue change for the EMV

put in a new one , and all is back to normal (: