Baking and Conditioning Part 2 of 2
Conditioning
The idea is that a new or cleaned liner, injection port, column, CFT device, or the MS ion source have some sort of exposed something-or-other that is chemically active to at least one of the compounds in the analysis. Conditioning is the word typically used to describe the process of resolving that by washing, rinsing, passivating, removing, covering, or somehow taking care of it so that the peak response is maximized and at least slightly more stable for unstable and reactive compounds. This is a bit like having a non-stick coating on the pan to save time during cleanup.
Conditioning the Injection Port
For liner and injection port conditioning, it is often suggested to run the normal method with about 100 injections of the high standard so that the active components fill up the active sites.
An alternative is to inject the high concentration standard at a high to very high split ratio to reduce stuff going to the MS. Use the normal analytical method’s final oven temperature and inlet temperature and set the injection port mode to Split and 2psi inlet, or as low as it will be stable, then 60 ml/min or higher split flow, 5µL injection (max with 10µL syringe on version of MassHunter I have loaded, at least), 2 second viscosity delay or more (always), and reduce injection dispense speed from the default 600µL/min down to something like 60µL/min (1µL per second) or even 30µL/min (0.5µL per second). This increases the sample exposure time of the liner, gold seal or MMI bottom, exposed end of the column, and the inlet body. It also reduces the number of injections to minimize coring the septum. How many are required? Who knows maybe have a sequence that does 20 5µL injections = 100µL total injected? Something should attach to any active sites after that amount of exposure. This can also be done manually using those inlet, flow, and oven parameters and slowly hand injecting about eight to ten syringes full of the high standard.
After one of these is done the inlet should be ready for calibration and sample runs. Don’t condition the inlet and then change the septum while the inlet is still hot as that will let oxygen into the liner/inlet/column/MS and defeat the process.
Conditioning the Column – see Baking the Column
“Conditioning the column” is often said when what is really meant is “baking the column to drive off contaminants.” Always purge the inlet and column thoroughly with carrier gas and verify that the system is leak free before heating them up. Wait long enough after new column installation and mass spectrometer pump down before checking this, though. If there is still oxygen in the system when looking for leaks the filament lifetime will be affected so wait at least an hour or more. Temperature programming to the bake temperature is not necessary. Stop conditioning when stable baseline is achieved.
See: beginners-guide-to-your-GC-columns-installation-care-maintenance
The fused silica used for columns is deactivated to enhance column inertness. All Agilent columns are pre-conditioned, pre-baked, during the manufacturing process.
See: Ultra Low-Bleed | GC/MS Columns | Agilent
And: Get the Most from Your MS Agilent J&W DB-5Q and HP-5Q GC columns
Conditioning the Source
The source is freshly cleaned. The oxygen has been swept out of the inlet, column, and vacuum chamber as the mass spectrometer is pumping down. The vacuum and temperatures have equilibrated longer than one hour. The Stainless Steel ion source may have exposed active sites but is not typically used for samples with peaks that degrade in the ion source. The Inert, Extractor, and High Efficiency Source (HES) have the critical parts made from a proprietary inert metal so should not need anything done to eliminate active sites. A very few, very active compounds may not show stable results with a freshly cleaned source. Some use the inlet conditioning method discussed previously, injecting the high standard mix many times. Some compounds require even more work.
With Hydrogen carrier gas and the SS, Inert, Extractor, and HES a very few, very active compounds may fragment differently so the resulting spectrum does not match library spectra created using helium carrier gas. Most analyses do not need perfect spectral fidelity, though, just stable response. If spectral fidelity for those very few, very active compounds is necessary, the HydroInert Ion Source may help. The HydroInert coating covers the metal so none will be exposed to sample molecules or ions.
Preparing the System to Run Samples
It is important to know how to optimize a system for the samples being injected. Understanding the effects of cleaning or replacing parts and how to resolve those quickly saves time.
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