Chromatography Forum

We just bought a new GCMS/MS we have been running the instrument in single quad just fine and retention times are stable. When switching into a triple quad method the retention times seem to shift all the time. I’m new to GCMS/MS are the retention times supposed to be the same as in single quad? What could be causing the retention time shifts in triple quad but not single quad?

In a GC/MS system it is the GC column that defines the retention time (RT); the mass spectrometer should not affect the RT of an analyte.

Now, the MS does operate under high vacuum conditions but I have never seen a comparison of GC/FID and GC/MS RT values to determine whether the high vacuum does help to pull the gas flow through the GC column more quickly, thereby decreasing RT values slightly.

There should be absolutely no difference in RT's between GC/MS and GC/MS/MS modes.

Can you give specific examples of your experiments (mass acquisition parameters in full scan GC/MS and GC/MS/MS modes etc) together with TIC and mass chromatograms??
Are you running EI or CI experiments??
Finally, are some analytes from a previous injection eluting in a subsequent run??

No reasonable difference should be observed in Rt on THE SAME SYSTEM using the same method etc. What you describe may be different. It sounds like you might be unfairly comparing TWO DIFFERENT GC - MS systems (?) and expecting the same results. The configuration, flow path, injector, columns (?), etc will be different in different GC systems. As such, different results would be expected. Each system must be optimized to the method and sample. The resulting data may or may not match. These types of analytical techniques may not produce identical data. Results are relative to the operator, instrument, software, sample(s) and/or total configuration of the system.

If you are referring to ONE GC - MS system where you are only collecting data from the first MS cell for some samples, then switching to MS/MS mode and collecting data, then you should see the SAME peak Rt for the same method and same sample (as nothing has changed, same instrument and method). If you see significant variation in Rt using any mode, this implies that your method is not rugged or reliable and the solution involves having someone experienced in GC/MS method development review the method and system set-up/configuration to find the cause.

It sounds like similar to what I do in setting up a method using the instrument in single quad mode first to develop the chromatography then switching to MRM to develop the MS/MS mode.

The retention time should not shift, at least not more than in the 0.01 type of range.

The one think I can think of, if it is and Agilent system would be the setting for the column outlet. If you don't tell it that it is sent to the MS the GC will assume atmospheric pressure at the column outlet and apply more pressure to achieve the desired column flow rate, in such a situation the change in vacuum when switching on the collision and quench gas could make a slight difference. On mine the vacuum increases from about 7^e-7 at 1.2ml/min to 5^e-5 with the MS/MS on and gasses flowing. I'm not sure that would cause a significant change in flow rate, and honestly temperature ramp rate makes more difference in retention time that small changes in flow rate does.

There should be an option for vacuum compensation in the gc program. Please check.

Triple quadrupole mass spectrometers have additional components and subway surfers complexities compared to single quads. These differences can affect ionization and ion transmission, potentially leading to variations in retention times.

(I am assuming a standard GC source and not some kind of APCI source.)

The method parameters should have a setting (checkbox) for "outlet at vacuum" or similar. Make sure that is checked 'on' for all of the methods using the MS. Sounds like there is a mismatch in the method parameters.

MS vs. MS/MS shouldn't have differences in retention times - That is a red flag for GC parameter settings problems.