Chromatography Forum

Hi all.

So: I'm a relatively experienced GC operator, new to the worldof MS, and I'm having some issues.

I have a new ScionSQ from Bruker, and have been trying to get it up and running. I had some challenges, the original column install had about 6" of column touching the floor of the oven, so we had some major bleed issues. I thought I'd cleared that up (took a meter off the column, baseline looked better each run), but it appears to be back with a vengeance. I'm kind of thinking it never really went away.

I'm getting an AutoTune failure--"Not enough ions to tune." If I turn on the MS in scan mode, and turn cal gas on, I see a peak at m/z 66....and that's it. Any clues? Is my column totally messed up and not actually flowing to the MS?

Apologies in advance, as I said, I'm a noob, and may have some silly questions along the way to taming this beast.

Cheers,

GCMSN

ETA: Air/Water report looks...funky. 28/32 ratio 35:1, 28/18 350:1, the absolute size of the 28 peak is 1x10^7, it tells me below 9x10^7 is acceptable.

Bleed issues: What is the quality of the carrier gas? Do you have an in-line fiter close to the instruument? Septum has been replaced reciently? What stationary phase are you running and how high a temperature are you running the column? What carrier gas are you using and what are you injecting?

Tune: Which cal gas are you using? Many instruments use PFTBA, which has a strong peak at m/z 69.

Bleed issues: What is the quality of the carrier gas? Do you have an in-line fiter close to the instruument? Septum has been replaced reciently? What stationary phase are you running and how high a temperature are you running the column? What carrier gas are you using and what are you injecting?

Tune: Which cal gas are you using? Many instruments use PFTBA, which has a strong peak at m/z 69.

Hi Don. Carrier is UHP Helium, through Bruker's multitrap, and through a nickel-based gas purifier after the instrument EFC, which eliminated some massive fluorocarbon signals. No septum, gas samples go into a cold trap and are desorbed onto the column (Valco setup). Column is HP-1, 30mx0.32 1.00DF. Symptoms were classic bleed, massive baseline rise above 200°C, MS says siloxanes and random siloxyl compounds.

I expected that the 69 peak was a part of the cal gas, but I see nothing at larger masses when tuning.

I'm planning to clean the source tomorrow, is there any reason I can't use 99.999% by residue reagent alcohol instead of MeOH for the last rinse? The place I work now is not a chemical company, getting new reagents can take some time. I also have access to chromatography-grade "hexanes" and ethyl acetate. I see Agilent recommends hexane as a final rinse with no bake of the parts.

I'm puzzled at how having a section of column touching the oven wall can cause bleed ? - if it was touching a heater element I could understand it, but, if anything, the section touching the wall will be cooler during a programme, not hotter.

If the MS is new it should still be under guarantee - get Bruker onto it.

You have a catalytic gas purifier after the EPC, and fluorocarbon contamination without it ? Does the purifier come as standard with the instrument ?

Peter

fluorocarbon signals after the EPC wiht high grade carrier gas? Something is wrong here. There should be no source of fluorocarbon signals in the pathway from the gas bottle to the GC column. If these relate to your samples, there is carryover and contamination from the sampling loop forward.

I commented on m/z 69, because I thought it was a different mass you mentioned in your original post - and I was wondering about major mass cal issues. So, how are vacuum levels for the MS running? And does your instrument have an evaluation of m/z 28 vs. m/z 69?

Bruker confirmed the fluorocarbons were coming from their EFC's, we are billing them for the purifier.

You're right, Don, it's showing up as m/z 66. I loaded an old tune file, still seeing about the same. New column should be here today. Unfortunately, they took out all of the vac sensors for this unit, Bruker service says the wattage measure I'm getting is "Perfect." No 28/69 evaluation.

I am starting to wish I were here for the purchsing process...

I know this will not answer all the questions but new filters are often filled with Nitrogen. He is difficult to keep inside the molecules are so small. The He filled birthday/happy occasion balloons ussually don't last too long. That's why the Nitrogen is in there.

This might explain why your N2 levels are up.

Loekie

Okay, I cleaned the source. Now I can see most of the cal gas peaks, still no m/z 502, autotune still fails.

If what is really m/z 69 is reading m/z 66, there is a major mass calibration issue. Can Bruker give any help with this?

I assume the instrument has tuned correctly in the past? Something is wandering and on a new instrument. I am surprised that the mass axis would be way off unless an error was made in setting tuining parameters or perhaps the electronics are wandering.

I loaded an old tune file, the mass is at 69 now.

Bruker is now telling me that having a leak for a while may have warped the filaments so that I'm no longer firing ions through the source. Does this sound logical?

As filaments age they may be sag or bow. I've pulled filaments out of HP and LECO instruments where I could see the distortion in the filament - and the instrument was still working reasonably well (I don't remember the qualificaiton for reasonable at the time).

My expectation with an air leak is for the metal in the filaments to sputter off the filaments, narroing the wire at some point and making a hot spot -- and that can affect instrument sensitivity. Typically you will see metal deposited as discoloration a short distance from the hot spot.

The solution for damaged filaments is to replace them. So, replace them and look at the old ones. If the filament is bowed or is eroded away by sputtering - it needed to be replaced. And, see if with a new, fresh out of the box filament will get the sensitivity you expect.

Okay, I don't think it's the filaments, then.

I have been getting good hardware diagnostics tests, then today I tried to cal the detector without tuning. It told me "No single ions found, gain too low, replace detector." How in hell could a detector burn out in two months??

Okay, I don't think it's the filaments, then.

I have been getting good hardware diagnostics tests, then today I tried to cal the detector without tuning. It told me "No single ions found, gain too low, replace detector." How in hell could a detector burn out in two months??

what was the voltage at on the multiplier (EM Volts) on the last successful tune? I doubt it's a bad EM but if major leaks and high signal are present then who knows.

Make very very certain you have no leaks around the inlet or the transfer line. I usually use a can of "Duster" which usually contains difluoroethane. This usually gives two masses between 28 m/z (N2) and 69 m/z (major ion of PFTBA). If you are in a Tune/Scan mode you can narrow in on this mass window and see the peaks increase as you spray the "Duster" over areas you may suspect a leak. I usually see leaks around the transfer line. Even when my N2 peaks are really low and I don't suspect a leak, I will still see the "Duster" peaks show a little bit as I spray around the transfer line nut.

The response around the transfer line is almost instant while it takes a few seconds to respond if you have a leak on the inlet side.

If you have a major leak then your filaments and possibly your detector may be bad. Don't toss the EM until you have verified through a "good" tune that the voltage is in excess of 2000 to 2200 volts. You may run higher than this on most instruments but you start to sacrifice sensitivity in this range.

I agree with everyone else. Bruker should step up and help out a little more with the issue. Agilent still helps me with my 6 year old 5973N MS when I have issues. They still provide phone support for free and I can call the field service techs when every I like (mostly because they are just good guys). See if you can contact the Bruker tech that installed the instrument. He/She should help you trouble shoot.