modes work TQ

Many operators want to be able to use a QQQ as if it was a Single Quad – they don’t always want to take advantage of MRM mode’s selectivity.   Which way should it be run, then – in MS1 Scan or MS2 Scan ?

Using MS1 for Scan and SIM:

When we use Q1 for Scan and SIM, we are using Q1 to filter the ions, which then impacts N2 molecules in the Collision Cell and go to Q2, which is in Total Ion Transmission (TTI – true total ion) mode.  We allow for the time delay of the CC and Q2 and measure the abundance.

Using MS2 for Scan and SIM:

When we use Q2 for Scan and SIM, we are using Q1 in Total Ion Transmission mode, so more ions make it to the Collision Cell, impact N2, get filtered in Q2 and then we measure abundance. It may produce distorted spectra of extremely fragile compounds that have trouble making it out of the source, fall apart before the CC, or fall totally apart in the CC.  This is partially due to the TTI cutoff. The 50 amu default is very acceptable for most as not many scan methods start below 40amu. It is not a hard/sharp cutoff and making it lower can cause strange effects.  Do not change the cutoff without knowing what you're doing ! 

MS2 Scan and MS2 SIM are better because of the differences in transmission efficiency of the quad in Total Ion Transmission mode versus the transmission efficiency of the quad when it is filtering ions.  Q2 has greater abundance, is less noisy, and suffers less from high-speed mass accuracy errors and resolution variation.

Also -- Never tune under one set of collision cell (CC) gas conditions and run (MRM, Scan, or SIM) under another due to the dramatic change in lag factors and sensitivity between CC flows on and off.  Also, it takes more than 15 minutes for the CC temperature to stabilize after flow changes.  The helium is there to reduce noise from helium metastables.  The nitrogen is there to fragment the ions further, which improves overall sensitivity.  If you change the flows, you have to retune the instrument.  If you do not, the mass assignments may be off because the lag factors from Q1 change with CC flow.

Should you wait for 15 minutes after, say, an Air/Water check where you turn off the nitrogen?  Well, you should wait, but only if you need to have perfect stability for more than one sample in that time --- so no one waits.

.

.

.

.

Many operators want to be able to use a QQQ as if it was a Single Quad – they don’t always want to take advantage of MRM mode’s selectivity.   Which way should it be run, then – in MS1 Scan or MS2 Scan ?

Using MS1 for Scan and SIM:

When we use Q1 for Scan and SIM, we are using Q1 to filter the ions, which then impacts N2 molecules in the Collision Cell and go to Q2, which is in Total Ion Transmission (TTI – true total ion) mode.  We allow for the time delay of the CC and Q2 and measure the abundance.

Using MS2 for Scan and SIM:

When we use Q2 for Scan and SIM, we are using Q1 in Total Ion Transmission mode, so more ions make it to the Collision Cell, impact N2, get filtered in Q2 and then we measure abundance. It may produce distorted spectra of extremely fragile compounds that have trouble making it out of the source, fall apart before the CC, or fall totally apart in the CC.  This is partially due to the TTI cutoff. The 50 amu default is very acceptable for most as not many scan methods start below 40amu. It is not a hard/sharp cutoff and making it lower can cause strange effects.  Do not change the cutoff without knowing what you're doing ! 

MS2 Scan and MS2 SIM are better because of the differences in transmission efficiency of the quad in Total Ion Transmission mode versus the transmission efficiency of the quad when it is filtering ions.  Q2 has greater abundance, is less noisy, and suffers less from high-speed mass accuracy errors and resolution variation.

Also -- Never tune under one set of collision cell (CC) gas conditions and run (MRM, Scan, or SIM) under another due to the dramatic change in lag factors and sensitivity between CC flows on and off.  Also, it takes more than 15 minutes for the CC temperature to stabilize after flow changes.  The helium is there to reduce noise from helium metastables.  The nitrogen is there to fragment the ions further, which improves overall sensitivity.  If you change the flows, you have to retune the instrument.  If you do not, the mass assignments may be off because the lag factors from Q1 change with CC flow.

Should you wait for 15 minutes after, say, an Air/Water check where you turn off the nitrogen?  Well, you should wait, but only if you need to have perfect stability for more than one sample in that time --- so no one waits.

.

.

.

.