Baking and Conditioning Part 1 of 2
GC and GC/MS samples come in all types, which is why the maintenance actions and frequency will vary. On GC and GC/MS systems little to no preparation to the system is needed for some sample types other than routine scheduled user maintenance. Some sample types need work done on the system before and after every sequence. Some sample chemistries are simple, straightforward, and robust, and some are complicated, head-scratching, variable, and reactive. The term conditioning is often used to encompass several ways to prepare a system to run samples including cleaning, rinsing, washing, baking, passivating, coating, deactivating, neutralizing, and probably others.
The following are often done on new systems or after typical user maintenance procedures have been completed.
When the installation is complete, the system has passed the required checkout procedures, and the engineer hands you the keys to your new system, your analysis may require the following steps. Very active compounds are found in most all types of analyses and these simple steps may get your system running samples sooner.
When typical user maintenance is done, especially inlet cleaning, column replacement, and source cleaning, these steps help remove any possible residue. Cleaning the inlet body and replacing the septum, liner, liner O-ring, and the gold seal should be completed as needed and probably more frequently than that. If the liner removed has visible contamination some has probably already gone into the column and so gone into the MS.
All Agilent GC columns are preconditioned, tested individually, and ready to run samples. A column that was removed and stored without capping/plugging the ends may need attention. A column that has been run for a while and shows high baseline or has contaminant peaks in a blank run will benefit. The blue total ion chromatogram (TIC) is a clean blank for this system. The red one is after someone did inlet maintenance just after touching some French fries.
For GC and GC/MS systems always ensure that there is no oxygen in the inlet, column, and detector before heating any of the zones. As little as 50 ppm of oxygen can cause irreparable damage to the column. Very low-level oxygen may take a long time to cause noticeable damage, yet it is important to minimize it as much as possible to increase the column’s lifetime.
Baking
Heating increases volatility, evaporation, vapor pressure, however you want to say it. Think about heating up a pan of stock on the stove to 80 °C, knowing that the water in it boils at 100 °C. That pan will go dry much sooner than a pan sitting at 23 °C room temperature. While reducing the stock to a sauce, that pan on the stove must have the lid removed so that the water/steam can escape or else it becomes a pressure cooker and does not reduce in volume. Blowing on it or fanning it will increase the evaporation rate, too. A wide shallow pan reduces the stock much faster than a tall skinny one because it has more surface area. Using a wide shallow pan on the smallest burner is slower than a lower temperature setting with the widest burner as more of the pan is at the necessary temperature. Sometimes a pan with a nonstick coating will save you time cleaning up.
Pressure increases the boiling point, and vacuum depresses the boiling point. At 15 psi gauge, 15 psi higher than atmospheric pressure like in an injection port, water boils around 121.3 °C (~250 °F). Under vacuum, like inside the mass spectrometer, the boiling point of water becomes difficult to calculate, but is somewhere lower than -50 °C (-58 °F). This means that baking the inlet is different from baking the MS.
Heating with gas flow or heating in a vacuum will drive off compounds that can be volatilized as long as there is a place for them to go. The pressure, temperature, and flow used will affect the speed and results.
Baking the Injection Port
Normal injection port (or inlet) maintenance. With the Split/Splitless injection port replace the septum, liner and O-ring, and the gold seal. While the gold seal is out, use three cotton-tipped solvent-dampened swabs held together to wipe out the injection port body. With a Multi-Mode injection port, replace the septum, liner and O-ring, and possibly remove the column and use three cotton-tipped solvent-dampened swabs held together to wipe out the injection port body and the brush from the MMI cleaning kit to clean the bottom of the port.
This procedure takes care of most inlet-related contamination. Put the injection port back together before reinstalling the column and turn on the carrier gas flow to purge out the cold inlet for a short time. Install the column to the proper distance, see: Column Installation - Split/Splitless and Multimode inlets =and= SQ and TQ MS transfer lines - Files - GC/MS - Agilent Community
Let the injection port and column purge for at least five or ten minutes or more before heating up the injection port and the oven.
If you think you need to heat it up, do not exceed the septum, liner O-ring, and column maximum temperature. Most Agilent septa can go to 350 °C and the preconditioned FKM (fluorocarbon) liner O-rings can go to 350 °C, so the limitation is usually the column’s max. Remember that whatever goes out of the inlet goes into the column where it may be difficult to eliminate.
Good inlet maintenance should preclude inlet baking.
Baking the Column – see Conditioning the Column
Heating the column does help get higher boiling point compounds, either sample or matrix related, to elute out of the column, just like reducing a stock to a sauce. The safest bake temperature is your normal run method’s final oven temperature. If that temperature is sufficient to get all the compounds of interest to elute it should be enough to get off everything else, too. A few degrees hotter is fine as long the temperature never exceeds the column’s isothermal maximum. Always purge the inlet and column thoroughly with carrier gas and make sure that there are no leaks before heating them up.
In general, do not condition a column into the oven before installing into the MS. This is especially true if you are using hydrogen carrier gas as conditioning into the oven is a safety hazard. Oxygen gets in the open end even as the helium is coming out and in a hot oven that will damage the stationary phase. The stuff also goes everywhere inside the oven and sticks on the outside of the column including the piece that you will then install into the MS. The stuff off that piece of column in the transfer line goes right into the ion source.
It is not recommended to condition some columns, for example Porous Layer Open Tubular (PLOT) or very thick-film columns, into the MS as some of those release particulates or bleed excessively during the conditioning process. It is also not recommended for all GC detectors either, as some have different issues handling column bleed. Read the recommendations in the data sheets that come with each column and the operations manuals for the GC detectors.
If there is concern about contaminants or column bleed getting onto the ion source, especially with the HydroInert Source, which cannot be cleaned, leave the ion source out of the MS while baking the column. Install the column, close the analyzer and pump it down, and use the GC controls. When complete set the oven temperature to near ambient then vent the MS, reinstall the source, and pump down again.
For timing, consider the number of column volumes being swept through. The internal volume of a 30 m x 0.25 mm id column is 1.473 mL. It should be baked long enough to sweep, what, 25 column volumes? 25 x 1.473= 36.83 mL at 1.2 ml/min is about 30.69 minutes. That is more than long enough. For 99.99% of applications, there is rarely any good reason to bake a column longer than 30 minutes or so. Conditioning a column too long can shorten the lifetime of the column if not done properly.
Using higher carrier gas flow while baking is like blowing on or stirring the stock. On a turbo system set the column flow to <= 4 ml/min (Max recommended gas flow on page 16 in the 5977C Operating Manual). You will need at least 80 psi supply pressure at the GC for this. Do not have the mass spectrometer’s filament on while the flow is so high. Twenty-five column volumes at this flow rate does not take very long, 25x1.473= 36.83 mL at 4 ml/min takes only 9.21 minutes.
One easy way to accomplish this is to set up a short post run bake-out to do this a little bit every run. In the Oven window, add a post run temperature and time and in the Column window increase the flow (see screen capture below). At the end of the analytical run, the MS will stop acquiring, the oven and flow will change until the time is over, then the run will complete and reset ready for the next run.
In the preceding example, 4 ml/min x 1.5 minutes = 6 mL = 4.07 column volumes of sweep every run.
The transfer line temperature should never exceed the column max. It does not need to be hotter than the final oven temperature, either, as the column part inside is under vacuum where the boiling points are all significantly depressed. The most logical transfer line temperature is to set it the same as the ion source temperature. Yes, there is an insulating ceramic tip seal between the transfer line and the source, but anything we can do to have a stable ion source temperature seems smart.
For more information, see Agilent J&W Capillary GC Columns Quick Reference Guide or A Beginners Guide to Your GC Columns: Installation, Care, and Maintenance.
Baking the Source and Quad(s)
Since everything that comes out of the column goes into the MS, that stuff is everywhere inside so a bit of baking seems smart. But do not forget about boiling point depression under vacuum. A favorite tool to picture this is Pressure-Temperature Nomograph Tool (sigmaaldrich.com). 313.6 °C under vacuum is like 700 °C at Standard Temperature and Pressure…and there are few compounds of interest for GC/MS that have a boiling point of 700 °C. However, the ion source and quad temperatures are only at the temperature setpoint immediately next to the heater/sensor. The farther away from the heater/sensor, the lower the temperature. This is like the small burner near one end of a large skillet. The handle end is cooler than close to the burner.
Because of this, it takes quite a bit of time for the analyzer to become thermally stable. Since the only heaters are part of the source and the quad radiator(s), heating them up heats up more of the analyzer and takes a while to reach equilibration or cool back down and equilibrated to be ready to run again. Before running samples, it is recommended to wait at least two hours after the source and quad(s) reach their requisite setpoints. Baking the source at, for example, 325 °C and the quad at 185 °C cannot hurt it…or can it? The end of the column coming out of the transfer line is right there so do not exceed that maximum. I do not like running the quad hotter than 185 °C but I have no real data for that, it just seems prudent.
In Single Quad Tune and Vacuum Control is a way to set up the source and quad to bake for a set amount of time. This is a great thing to do before a weekend so that the system is ready to go Monday morning.
For single quad systems, there are a few ways to automate this. One is to use the Sequence Table Keyword “Bake.” It uses the temperatures and time entered using the Bakeout MSD… parameters entered as shown before. The software remembers the entered parameters even if you choose No to “Start bake-out procedure now?”.
This sequence table will do three sample injections and then run the bake out procedure and load the method specified after the bake-out has completed.
In triple quadrupole Vacuum Control, it is like this:
The Bake Sequence Keyword is not available for triple quadrupole systems. One way to automate the bake is to create and save a tune file with the requisite temperatures and create a method that points at that tune file. In that method, enter something like a 2-hour run time and a 1 hour and 59 minute solvent delay so that the system only captures 1 minute of data. Add this method as the last line in the sequence.
Conditioning to follow in Part 2.
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