Chromatography Forum

Our lab just bought a second-hand LC/MS (agilent 1100 LC with API 2000 MS). The technician from the vendor installed, tuned and gave us a basic trainning on it. However, when I started doing some test runs, I got very high basline noise (10^6, sometimes 10^7), and the major peaks are m/z 65, 83, 93, 97, 125, 129. After some digging, I found the m/z 65 may be caused by dimerization of methanol (2M+H), but I can not figure out what causes the problem and how to solve it. No one in our lab knows how to use MS. Therefore, I need help please!

Thanks

Our lab just bought a second-hand LC/MS (agilent 1100 LC with API 2000 MS). The technician from the vendor installed, tuned and gave us a basic trainning on it. However, when I started doing some test runs, I got very high basline noise (10^6, sometimes 10^7), and the major peaks are m/z 65, 83, 93, 97, 125, 129. After some digging, I found the m/z 65 may be caused by dimerization of methanol (2M+H), but I can not figure out what causes the problem and how to solve it. No one in our lab knows how to use MS. Therefore, I need help please!

Thanks

Mayber there is no real Problem?

I don’t know this system and cannot judge if the noise is normal or abnormal for this system and your conditions. But it is not uncommon to observe much noise with lc/ms especially when you start your scan-range with m/z 50 (many applications start with m/z 100). Therefore using background-subtraction is often done for lc/ms if you want to have nice mass spectras.

The mentioned dimerization of methanol is very common, depending on system, ionization-technique, tuning and used chemicals you observe often ion-cluster builded from you mobile phase (also Na+, K+; NH4+ is almost everywhere) and/or your analyte.
Maybe you should get a documented application for your system and try to reproduce it in your laboratory with your system.

Our lab just bought a second-hand LC/MS (agilent 1100 LC with API 2000 MS). The technician from the vendor installed, tuned and gave us a basic trainning on it. However, when I started doing some test runs, I got very high basline noise (10^6, sometimes 10^7), and the major peaks are m/z 65, 83, 93, 97, 125, 129. After some digging, I found the m/z 65 may be caused by dimerization of methanol (2M+H), but I can not figure out what causes the problem and how to solve it. No one in our lab knows how to use MS. Therefore, I need help please!

Thanks

Mayber there is no real Problem?

I don’t know this system and cannot judge if the noise is normal or abnormal for this system and your conditions. But it is not uncommon to observe much noise with lc/ms especially when you start your scan-range with m/z 50 (many applications start with m/z 100). Therefore using background-subtraction is often done for lc/ms if you want to have nice mass spectras.

The mentioned dimerization of methanol is very common, depending on system, ionization-technique, tuning and used chemicals you observe often ion-cluster builded from you mobile phase (also Na+, K+; NH4+ is almost everywhere) and/or your analyte.
Maybe you should get a documented application for your system and try to reproduce it in your laboratory with your system.

Thanks for your suggestions.
I washed the LC with pure methanol for 2 hours, ran a blank with just solvent and the baseline was back to normal (about 200). However, when I tried again with standard PPG, the baseline went back to 10^7. The same baseline with running pure solvent. Maybe it was the sample got heavily contaminated. I will try to flash the LC again and remake the PPG to see if it will help.

Can anyone give me some suggestion about how to make up samples to make sure they are contaminants free?

What is meaned with "PPG"?
Whast is you sample?
Have you ever tried to reproduce a application example from the lc-vendor?

Are you based in China or US?
Best regards
Klaus

What is meaned with "PPG"?
Whast is you sample?
Have you ever tried to reproduce a application example from the lc-vendor?

Are you based in China or US?
Best regards
Klaus

The PPG is the standard example used for tuning the ATI 2000, and we aquired the sample from the vendor. Like I sait in the previous post, I tried to inject pure solvent (water), it still came out with noisy baseline. I only managed to get one spectrum with low noisy basline and I do not even know how I got it.

I am based in Canada.

Thanks

"Noisy baseline" is not enough information to solve the problem.

Please describe in detail and step by step what are You trying to do. Injecting the sample trough the HPLC or directly using syringe pump? Are You sure sample concentration and all the parameters are correct (also MS voltages etc.)? Too concentrated sample solutions can contaminate spray or electrodes and cleaning of the parts might be necessary to remove this. Could it be that incompatible with MS solutions (phosphates atc.) were injected accidentaly?

Did the problem appear next day the service left or instrument was standing idle (was switched off completely?) for some time?