intermittent sharp peaks in the background of GC/MS

[2fhk]

I don't know why I have so many intermittent sharp peaks in the background.
I don't think these peaks are due to the injection part, because the m/z 28 and m/z 32 appear at the same time. I also noticed that the ratio of m/z 28 to m/z 32 is about 2: 1 in the background (the same as the ratio shown in air and water leak check). However, the intermittent sharp peaks showed a ratio of m/z 28 of around 1.1: 1.

Does anyone has any idea what is causing the problem?

Please see the shared files for the snapshot and the tune report for more information.
https://drive.google.com/drive/folders/0B-e4IRzSPpd7TElvb2ItUGJUYWM?usp=sharing

[James_Ball]

What is the oven temperature during that run of the baseline chromatogram?

Is there anything above 44m/z in the background at the 8.8 minutes mark you have displayed?

If that background is entirely what is displayed in the spectrum window and the background is 300,000 counts, what is the electron multiplier setting during that run?

From looking at the spectrum and the mass counts there, it would appear it is mostly the m/z 28, 32 and 44 that is giving the 300,000 count background. I notice the Autotune spectra has almost 3,000,000 counts for 69 at 1859 volts on the electron multiplier. That is super sensitive, we normally run with 69 at anywhere from 300,000 counts up to 800,000 counts. You could probably drop the multiplier voltage down to 1600 volts and lose most of that background and the spikes would barely be visible if at all. They could simply be some electronic noise with the gain set that high which is not unusual for an older instrument like the 5971.

Try backing the voltage down until you have only 28, 32 and 44 appearing in the background with a threshold of about 100 which should be when you get the 69 below 500,000 counts, and see if you notice the spikes then, and you will probably gain better signal to noise ratios between your background and your target peaks, even though the total counts will be lower, which will give you better low end sensitivity and more linear range for the analysis.

[2fhk]

@ James_Ball
Thanks so much for your reply.
For you questions,
- During that run, the oven temperature is 50℃, the EM voltage is 2071.
- There is no major m/z above 44.
- I tried lower the EM voltage to 1600, the background dropped to 150,000 and I still see the spikes.

[Rndirk]

My 2 cents. I think "peak" is a misleading term in this case. From the zoom in on the chromatogram, it is a single point. I would not conclude from that chromatogram that there is anything eluting at that time. It seems more mass spec noise (like James said).

Do you need to measure below 44 m/z in your analysis? If not, i wouldn't worry about it too much.

I'm not familiar with the 5971. What is the Xray setting in the tune? Is the MS temp the source or quad temperature?

[2fhk]

Thanks for your reply！
Both James_Ball and Rndirk is right!

I did two things,
- Lower the EM voltage
- Only detect ions of m/z > 35, since I don't really care about too much about m/z <35.

Finally, no spikes and the background is lowered to around 10,000.

Thanks again!
This is my first time asking questions and I appreciate your help so much!

[2fhk]

Thanks for your reply！
Both James_Ball and Rndirk is right!

I did two things,
- Lower the EM voltage
- Only detect ions of m/z > 35, since I don't really care about too much about m/z <35.

Finally, no spikes and the background is lowered to around 10,000.

Thanks again!
This is my first time asking questions and I appreciate your help so much!

[James_Ball]

My 2 cents. I think "peak" is a misleading term in this case. From the zoom in on the chromatogram, it is a single point. I would not conclude from that chromatogram that there is anything eluting at that time. It seems more mass spec noise (like James said).

Do you need to measure below 44 m/z in your analysis? If not, i wouldn't worry about it too much.

I'm not familiar with the 5971. What is the Xray setting in the tune? Is the MS temp the source or quad temperature?

Xray on the 5971 is similar to the HED on the newer models, but it was adjustable on those and ran at a much lower voltage.

Also on the 5971 there were not heaters inside the MS, but there is a thermocouple attached to the radiator near the source interface and the transfer line heated the source through conduction and the temperature usually ran around 170C if the transfer line was set to 250C.

[James_Ball]

Thanks for your reply！
Both James_Ball and Rndirk is right!

I did two things,
- Lower the EM voltage
- Only detect ions of m/z > 35, since I don't really care about too much about m/z <35.

Finally, no spikes and the background is lowered to around 10,000.

Thanks again!
This is my first time asking questions and I appreciate your help so much!

10k is a good background when it is running as clean as your system seemed to be from the tune file. With the lower voltage you will have more linear range and the multiplier horn will last longer too.

[Bigbear]

You can also set the lower scan mass to 35 as you say you don't need to see below 35.