Chromatography Forum

I am the new operator of an old Leco Pegasus III mass spectrometer. Unfortunately its previous operator died of cancer after struggling 4 years with it. When I turned the instrument on after 4 years I saw PFTBA 69 peak is very weak. Took a sample acquisition and saw other light ions strong peaks are there. So detector is OK and haven't seen air. Tried to run Optimization but after passing a few steps stopped on resolution step with "user terminated". It needs at least signal/noise=300 to pass but highest it goes is 70. I removed PFTBA glass bulb and checked inlet line and I noticed there is a brass "piece" in the PFTBA inlet line, connected between the glass bulb and the electric inlet valve (the one you hear its click sound when you do instrument optimization). It looks blocked and I surprised how PFTBA can flow through it?. I guess these should be a small nano filter or plate must be inside. I have very small 69 peak (about 10000 count) which shows almost no PFTBA goes inside because other strong peaks are there. I want to give it a try and clean it and see if I can get the 69 peak back but don't know how. Used isoproponal on one side but haven't seen any on the other side. Put some pressure and saw it got wet on the other side. Any more suggestion how to clean it? Anyone noticed this ever?

Contact LECO service. From my experience, they will talk to you -and unless things have changed in the past few years, they will talk to you even if you are not under contract. It has been years since I've had the PFTBA vial apart on a Pegasus, but I do recall a frit in the path - I don't remember if it was brass or housed in a brass part.

What you have not described are 1: vacuum reading 2: indication of air leaks or not 3: detector voltage. If the instrument has sat without proper vacuum for four years, the detector may be damaged from excessive exposure to air.

And, on putting that bulb back into the fitting - If you have the teflon ferrule, check to see if you have a fresh one. They deform easily. And wyen youput the fittign together, make sure the glass bulb is nto pushed all the way into the fitting. Bottom it out and then pull back about a milimeter. The ferrul compresses - the glass does not. The glass makes this distinctive crunching sound rather than compressing. And if you do not get the depth right, you can even crush two in a row (not that I'd know ). Again, a call for a bit of help could save you the cost of a part or three.

It is housed in a brass part. I can see the little graphite cylinder at the input side but no see through hole there inside. Detector is ok and all voltages are ok. peaks are all there except PFTBA peaks which are very weak. That is why tuning fails at resolution optimization.

I talked to Leco and they said it is a restrictor and need to be replaced. A new one ordered but for my curiosity I will find a way to clean it and see how it will go. It is not expensive but is good to understand what is happening inside this little thing. Forgot to ask them the diameter of the hole inside but I think should be around 0.1 mm comparing with Agilent quickswape restrictors.

Thanks Don.

As you said it was a stainless steel frit. After cleaning with acetone PFTBA peaks came back nicely.

I noticed there is a FID detector factory installed on the Agilent 6890 GC. It is not connected anywhere. I wonder why it is there with this instrument. I am thinking about using it with a second column, the back injector and Chemstation software just to have a look at the rephotograph before letting unknown nasty samples get into the MS and cause its unwanted contamination. Please welcome to comment if you confirm this and if you think this is a good idea?

I have had several instruments over the years with an unused FID and an active mass spec. The reasoning in purchasing the FID was that it would be available if something happened to the mass spec or for trouble shooting. (And was never used.) I have seen a GC injection split such that the column eluent was split between the mass spec and another detector. In a lab that I worked in this other detector would typically be a selective detector, such as NPD.

If you add a second column to the GC, the instrument is tied up with GC-FID runs when you could be using it for GC/MS runs.

With other GC/MS instruments, you try to avoid putting a lot of stuff down the column because the ion source needs to be cleaned more frequently. The Pegaus has a source design that LECO advertises as never needing cleaning. And, I have used several Pegasus instruments for years without source cleaning.

In the lab that I am in now, I use the Pegaus GCxGC-TOFMS for samples that may be nasty. I use a liner packed with wool and keep the inlet temperature lower than the maximum column temperature to avoid transferring stuff that will never elute from the column. My objective with these samples is to make sure that I understand the sample matrix before taking the samples to a GC/MS/MS or GC-HRMS, where we will be blind to what is going on with the matrix as we look at a narrow mass range in obtaining the sensitivity we need. I take advantage of the good sensitivity for full spectral range acquistion afforded by TOFMS.

I have had several instruments over the years with an unused FID and an active mass spec. The reasoning in purchasing the FID was that it would be available if something happened to the mass spec or for trouble shooting. (And was never used.) I have seen a GC injection split such that the column eluent was split between the mass spec and another detector. In a lab that I worked in this other detector would typically be a selective detector, such as NPD.

If you add a second column to the GC, the instrument is tied up with GC-FID runs when you could be using it for GC/MS runs.

With other GC/MS instruments, you try to avoid putting a lot of stuff down the column because the ion source needs to be cleaned more frequently. The Pegaus has a source design that LECO advertises as never needing cleaning. And, I have used several Pegasus instruments for years without source cleaning.

In the lab that I am in now, I use the Pegaus GCxGC-TOFMS for samples that may be nasty. I use a liner packed with wool and keep the inlet temperature lower than the maximum column temperature to avoid transferring stuff that will never elute from the column. My objective with these samples is to make sure that I understand the sample matrix before taking the samples to a GC/MS/MS or GC-HRMS, where we will be blind to what is going on with the matrix as we look at a narrow mass range in obtaining the sensitivity we need. I take advantage of the good sensitivity for full spectral range acquistion afforded by TOFMS.

As for dual column analysis with the FID and MS, it could easily be done if the software would accept both signals at the same time. I know when using an Agilent MS I have done this. Use the same column in front and rear detectors, inject both columns and acquire both MS and FID data. You can run a set of samples first on the FID to screen then the next day run them on the MS while running the next set of screens on the FID. The disclaimer would be that this was back on the Win3.1 or Win95 version of Chemstation I believe so not sure it still works this way or not. Been a while since I did that setup obviously.

With a Pegasus instrument, you are not going to get far with ChemStation. But I've seen ChromaTOF (The LECO aacquisition software) handle this just fine.

Regarding FID when I choose GC method in Chromatof, I see transfer line temperature is required to be filled in the respective pane .This means even in GC method Pegasus III collects data from mass detector and I see no way of collecting data from FID detector with Chromatof. It seems in any method Chromatof collects data from mass detector via channel board and if I want to use FID I have to install Chemstation which is not shipped with the instrument. Am I right or am I missing something here?

ChromaTOF has (or had) a way to pick up an additional signal beyond the MS signal. And, I've seen it done and discussed the difference in retention time between MS signal and FID signal with the person who had it set up. (This is normal when you split the column between a detector under vacuum and one at atomspheric pressure.) I unfortunately do not have contact information any more.

I don't have a copy of ChromaTOF handy (I'm at home). But if you call LECO service, they should be able to help you. If that fails let me know which version of ChromaTOF you have and I'll see if I can get a few minutes at work to do some looking. My email is dchilton at mylink dot net.

I am using Chromatof version 2.0 . I have sent an email to Leco yesterday but it is too soon to have a reply from them.

I had the nice 69 peak of PFTBA the other day after cleaning the frit in the PFTBA path along with all other peaks of PFTBA and all three optimizations finished successfully with no problem. Turned Instrument off for about a week. Today I turned it on and tried to do optimization again but I saw very small 69 peak and instrument didn't pass even first focus step (very low sign/noise, below 300. minimum need=1000). I checked PFTBA level in vial and it is ok. Also background check looks ok (all background peaks are there). The only problem comes to my mind is failure of the tiny 24V PFTBA electric valve. I hear its click sound when I click "optimize now" but it seems it does not open in reality. Anyone has the experienced the same problem and replacing this valve? It looks very strange to me. Never imagined this valve may fail. It is expensive so I want to see if anything could be done before ordering a new one. I may temporarily use a manual shut off valve for now before ordering a new valve and open it manually immediately after clicking "optimize now" and close after optimization finished.

Also still waiting for advice about how to acquire data from GC 6890N FID detector with Chromatof software?

Yes it was because of the isolation electric KIP valve. Someone from Leco changed it and left. When I was connecting PFTBA vial I picked the without frit connector by mistake. When I did optimization a large amount of PFTBA went in and everything including detector turned off right away automatically. I had to wait overnight before I could get a proper optimization peaks again. First two optimization steps succeed but mass calibration failed because detector noise seems is too high. I guess I have to wait a few days for detector to recover to a lower noise level then try mass calibration again (through acquisition system adjust of course). Has anyone experienced a Lot of PFTBA going inside the mass? This is the first time it is happening to me. I am waiting for advice from people who the same experience to let me know how to deal with this.

It was late and I couldn't ask Leco engineer to wait for optimization and he had to leave. I might ask him to come back if I couldn't get mass calibration to work in a few days.

Given that it takes at least four hours for an instrument to be sufficiently under vaccum to operate - I can see the engineer not staying on site. Had you removed the PFTBA vial and frit before the engineer arrived? Some engieers will not reinstall something you have removed. And, a company can not take responsibility if the customer has swapped one part for another (like accidentally hands the engineer a frit adapter with no frit) and the instrument fails after the wrong part is intalled. (Other engineers will put the parts together, just to avoid the return trip when the customer breaks somethign while putting parts together --- but eventually they learn that this is a risky situation.)

If you are set up to vent with dry nitrogen, you can have the system back up and running in about an hour, but not everybody has this. And this is still an hour. This repair is pretty simple -- the valve either works or it doesn't. And chances that the new valve works are extremely high.

I am a bit puzzled as you describe having the instrument turned off for a few days and then turning it on. I hope that you leave the instrument powered up, pumps runnign and source hot when not in use. Mass spectrometers do not like to be left powered down - no matter what make they are. Keep the GC turned on and at least low flow through the system to keep from pulling air in through the split vent and septum purge. Teh GC inlet must be sufficiently above atmospheric pressure to avoid significant diffusion of air into the inlet - or you need a high enough split rate to keep significant air from entering the inlet. You want to keep the transfer line hot - but avoid oxidation of the column. Cycling the temperature on the transfer line is a way to have the graphite/vespel ferrule on the end of the transfer line fail. Not hard to fix - tighten the nut. But if you have the GCxGC system installed - you have to get to the nut. Again not hard, but it takes time that I'd rather be spending on other things.

I told Leco engineer about cleaning the frit while he was changing the valve. He said one way is using dilute nitric acid in ultrasonic. After installing the valve I told him not to install the frit and vial. I wanted to do another cleaning of frit in ultrasonic and nitric acid. I cleaned the frit but somehow at the time of installation I picked the wrong adapter. I am surprised myself how this might have happened. Never happened before to do such mistakes.

I have Argon gas setup and I can purge the chamber with argon gas if it is supposed to left unused for a long time.

Ion source as I understand will not stay hot because after standby time elapsed instrument will turn the filament off automatically but letting small amount of carrier gas to go inside the chamber for not letting air sucked inside through inlet and septum is a good idea. I was thinking about putting a 4 way valve inside GC in the column path towards MS. Connecting that side of the column that goes inside MS to the input of this valve and then one utput can go inside MS through transfer line and one into FID detector and the other into exhaust. This way I can completely block MS input when it is not in use by this manual valve or want to change the column. Letting He gas to go inside the chamber when not in use can cause extra load on turbo pump which I don't like it. Another advantage of using 3 way valve is obtaining high vacuum inside the chamber when not in use which can cause cleaning of the chamber.

I forgot to ask the engineer about how to use FID with Chromatof