Chromatography Forum

Hello Chrom nerds I need some help

I am helping a friend out with their Advion LC-MS it also has a DAD before the MS.

I have got the sources working, he had been having trouble keeping good tunes. But now that we have good tunes the analytes that are clearly visible by DAD are completely non existent in the MS. I am figuring we are having some trouble with ionization, but the fact that we are seeing peaks fine in our tunes makes it hard for me to think on how we can remedy the issue.

There are also some serious contaminant peaks that show up across the entire run with counts in the millions. I'm honestly not sure how to get these out. I am worried that the Quad is dirty and unfortunately I highly doubt Advion would guide me through a quad cleaning.

Any guidance or thoughts are appreciated

Hello Chrom nerds I need some help

I am helping a friend out with their Advion LC-MS it also has a DAD before the MS.

I have got the sources working, he had been having trouble keeping good tunes. But now that we have good tunes the analytes that are clearly visible by DAD are completely non existent in the MS. I am figuring we are having some trouble with ionization, but the fact that we are seeing peaks fine in our tunes makes it hard for me to think on how we can remedy the issue.

There are also some serious contaminant peaks that show up across the entire run with counts in the millions. I'm honestly not sure how to get these out. I am worried that the Quad is dirty and unfortunately I highly doubt Advion would guide me through a quad cleaning.

Any guidance or thoughts are appreciated

When you tune, are you doing direct infusion? If so, try running some of the tuning solution through the same setup and see what happens.

Regarding the contamination, how have you cleaned everything up to the quad? Quads aren't too difficult to clean but their positioning can be problematic. Thermo has this to clean a quad:
1. Use a soft brush to scrub the inner surface of the rods with a 1% solution of Liquinox in water for 10 minutes.
2. Use a soft toothbrush and a 1% solution of Liquinox in water to scrub
each end of the quadrupole for 5 minutes.
3. Use a soft toothbrush to scrub the outer surface of the quadrupole for
5 minutes.
4. Rinse the quadrupole thoroughly with water.
7. Rinse the quadrupole with methanol.
8. Blow the quadrupole with a stream of nitrogen gas until it is dry.
9. Examine the quadrupole. Ensure that no particulate is present.

Hopefully there's something here that's useful!

I think you may be missing some training and/or a basic fundamental of chromatography. Just because you detect "peaks" via DAD (UV/VIS) does NOT mean that you will or should see peaks by MS. They are two completely different things. Many compounds do NOT ionize at all or not ionize well enough,under the conditions used by the MS (Using YOUR settings and your method. Millions of possible MS methods and parameters to consider). The tune mix is only used to establish that a small group of KNOWN standards will ionize and provide output data that is similar to a stored set of data. The tune standards are not your samples. Any output observed from the 'tune' mix is not relevant to your samples. Running the tune mix only establishes that the instrument (detector) is setup using a specified data set and will output an expected result, within an acceptable range. We use as a check to confirm that the basic operation of the detector is reproducible. The standards used for "Tune" as specifically selected to show great signals, ionize really well over a wide range of parameters and be easy to setup. Due to structural differences, AND ESPECIALLY the HPLC Method conditions used (change the flow rate or mobile phase and you change the MS results), many sample types will be detected differently, requiring completely different MS settings to see peaks. MS is NOT a universal detector. They can not detect so many types of samples at all. Just as with UV/VIS, there are many sample types that can not be detected. We couple the two detectors, inline, because of these differences. Often, if the LC-MS method is well developed, you may acquire useful data from both detectors. However, it is normal to not see any data for some peaks due to their actual concentration levels, structure or suppression during analysis.

To determine IF your actual samples can be detected by your specific MS system under HPLC conditions an infusion of sample liquid should be set up first. Use a syringe pump and a solution of your sample. Have an experienced chromatographer, who has many years of practical industrial experience using the specific MS detector, set up a screening run in real time while infusing sample. Careful, do not overload the source (contamination!!!). This will allow you to change the MS parameters in real-time to see where the true baseline noise level is, what types of parent ions (or fragments) are detected, then start to optimize the settings to detect the compounds of interest. If detection is poor, then adducts[ [https://hplctips.blogspot.com/2011/12/a ... s-esp.html ] can be formed to improve the signal If done correctly, you will learn a lot about the sample material and can then develop a proper HPLC-MS method which retains,separates individual peaks than elutes off the compounds. This will allow data to be collected.

Lastly, please have the instrument professionally cleaned, serviced and checked before use. Trying to use an LC-MS w/o the basic training (which takes several years) is prone to error and misleading results. Start with a clean, functioning system so your time and money are not wasted.