Difference between first and second channel in MRM-function

[leka]

I've posted this question in another discussion in this forum called "Drift in LC-MS despite isotope internal standard" but since this phenomenon might be unrelated to the original problem in that thread I start this new thread:

We have a LC-MS-MS-analysis with two MRM-functions. We've inserted two "dummy" channels in the beginning of these MRM-functions and it seems as there is a big difference between the first and the second channel: the area of the analyte in the first channel is 2-4 times higher than the area of the analyte in the second channel. And the difference between the two channels are just 0.01 Da (e.g. we monitor 162.05>84.89 in the first channel and 162.05>84.90 in the second), i.e. the first channel is really just "repeated".

These "dummy" channels make it possible for us to use the second channels for quantification, i.e. the first channels give (most of the time lately) not only higher areas but also false results.

We tried to prolong the interscan delay from 100 ms to 200 ms, but the phenomenon persisted.

We have carried out test on another analysis running on the instrument. We "repeated" transistion 301>72 and transition 315>86 in two different experiments: no difference in area between the fist and second channel.

Does anyone have experience in this? Any ideas what might cause this phenomenon?

[leka]

Hi,
The problem is now gone.

We had a thorough cleaning of the mass spectrometry done. This included the collision cell, hexapole and source but also removal of visible marks (ion burns) at the first quadrupole.