Peak shape issues

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

12 posts Page 1 of 1
Dear community,

after solving the noise issue on our Agilent MS7000a system, we still have problems with the peak shape. We noticed deteriorating peak shapes for quite some time with a rather wide range of analytes (also before the noise issue came up).

Image

This example of an alkane standard mix was measured without time filtering. When I activate time filtering (I think it's on by default), the peak shape is almost perfectly Gaussian. I find this worrying since we may have been experiencing this issue for quite some time, but nobody may have noticed since time filtering was on all the time.

Agilent have suggested that the Quad 1 may need to be cleaned, as the abundances of the higher m/z in the tune are way lower in the Q1 compared to Q2. I would not rule that out but our samples are usually really clean and do not contain much dirt. From my understanding the quartz/gold quads should not require cleaning.

The most recent tune report can be found here.

Another diagnostic would be that the filament current fluctuates between 34.9 and 35.2 µA. Agilent say that fluctuations of +/- 1 µA may cause zig-zag peaks, but this should not be an issue in our case.

The ion source is clean and switching between the brand new filaments does not change anything with regards to the peak shape.

Any tips regarding trouble shooting are highly appreciated.

Thanks,
cb23
What mass of alkane is in that peak ?

Peter
Peter Apps
In that sample we have about 200 µg in 200 µl toluene, 1 µl injected in splitless mode
cb23 wrote:
In that sample we have about 200 µg in 200 µl toluene, 1 µl injected in splitless mode


That's 1 ug on the column and into the MS, so the raggedy top might be detector overload. How does it look at a 10:1 and 100:1 split ?

Peter
Peter Apps
Peter, I have to apologise, it is a 10:1 split, indeed.
Not likely to be detector overload then. What is the column temperature programme, inlet temperature and transfer line temperature ?. Do all the peaks in a series of alkanes look the same ?.

Peter
Peter Apps
My impression is that the ugly peak shape occurs irrespective of oven programme, split settings, etc.

The peak shapes are bad for all alkanes no matter the chain length.

GC maintenance performed so far on the 7890 GC: Inlet cleaned with FID brushes and solvents, new liner, new gold seal plus washer, new nuts and ferrules, split vent line rinsed, new filter cartridge. First column cut (1 metre or so). We run samples on a combination of first DB5, then DB1 connected by a press fit (each is 15 m). Air water check is fine.

Regarding the liner: we clean them manually, i.e. KOH + H2O2, rinse with demin. water, acetone p.a., then silanise at least for a week in 5% dimethyldichlorosilan in toluene. After than we rinse them with MeOH, toluene and pack them with "a little ball" of silanised glass wool.

The GC params are:
Inlet 280 °C
We run them splitless or 1:10 split.
Carrier gas is helium at 1.17 ml per min
Aux heater is 270 °C

Oven programme:
80 °C for 1 min
#1 then 10 °C/min to 150 °C for 0 min
#2 then 1 °C/min to 275 °C for 0 min
#3 then 10 °C/min to 300 °C for 10 min
The only thing there that might distort peaks is having two columns connected together - but I would expect any effect to be tailing rather than ragged tops. Even so, before you do any more with the MS it might be worth running with only one column.

Another possibility, and easy to check, is that the column is touching the oven wall somewhere, creating a spot with uneven heating.

Peter
Peter Apps
Peter, yeah, the column was touching the oven wall a few times... I have corrected that.

Also I have now swapped the ion source of our 5977B with the one in our 7000A. The source heater of the 5977B said "SST EI 350", while the 7000A's said "Inert EI 350". Agilent said that they are compatible. However, the 7000A's also got an extractor lens, which the 5977B has not got. Not sure if it will tune without an extractor?!

Could I ask something maybe stupid: Can you run a triple quad MS in single quad mode? Given that the Quad 1 is dirty or malfunctioning, can you do all filtering on Quad 2?
I'll leave the question about running a triple quad as a single quad to the people who work with that kind of hardware.

It's a pity you moved the column off the oven wall and changed the ion source at the same time - rule 2 of troubleshooting is to change only one thing at a time.

Peter
Peter Apps
I haven't found a way to use the final quad on the 7000 yet, except in tune mode. On the ABI3200 LCMSMS we have you can scan with either quad, but not on the Agilent7000. You can use normal Q1 single quad mode on the 7000 and it works just like a normal single quad instrument, I do it for most of the work done on our 7000.

Is the abundance on that peak in the photo at 10e8, I can't seem to zoom it enough to make it out on my screen. If so that it getting up there to the point of saturating the detector.

The Time Filtering is used to smooth the chromatographic peaks so maybe turning it off is what is causing the problems, the help for that mentions this

"Select to apply a Gaussian filter to smooth the chromatographic peaks. Sets the filter to the Peak Width (sec) entered below. This value should be approximately the full width value in seconds at half the maximum height for your narrowest chromatographic peak."

Almost all MS data is smoothed by default, but on Mass Hunter you have the option to turn it off. I know on our LCMSMS that when you are just looking at raw data, the peaks can look very rough, even with good chromatography, and we normally apply the smoothing in data analysis. Agilent usually applies the smoothing by default in most cases.
The past is there to guide us into the future, not to dwell in.
Sorry for the low quality, in fact it is 10e5, so no detector overload, I guess.

Today I ran a tune and samples with the 7000a ion source built into the 5977B MS (with the extractor disconnected). Both tune report and sample look brilliant. I guess that means that the 7000a's ion source is perfectly OK and the bad peak shape is due not due to the detector or ion source.

Regarding the quad selection, that is really a pity... After manual tuning I got the impression that it may be in fact possible to run it in single quad mode on quad 2.

Regarding the time filtering, also Agilent have suggested to keep time filtering on since it appeared to solve the problem. The thing is, that the peak shape used to be really normal a few months ago and now it is getting worse and worse.

Peter, yes, I realised that also of course, but it was too late already, bummer. However, I will swap the ion sources back later today. Basically, all I wanted to know is if the ion source was causing the problem....

Thanks a lot so far to everybody who contributed. If the the peak shape is still not good enough after putting back the source and fixing the GC column touching the oven walls, then I need to call Agilent for a repair....
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