Hi,
I have recently performed metabolomics. But, I am finding some difficulty. I have encountered PEG contamination. Although, I am using MZmine software and able to SCREEN out contaminants.
I have some questions. I believe that since I am using LC-MS grade reagents, I should not have contamination from them. I believe the PEG contamination comes from cell scrappers/eppendorf tubes.
Any suggestions from where can I but PEG-free materials like cell scrappers and eppendorf tubes.
I understand this is not science but it is also a part of research.
Regards,
Pratik
First thing to do is make sure your solvents are really clean of PEG. There are bad batches and there are manufacturers that sell LCMS grade solvents that really aren’t suitable for LCMS work.
Edit: That said I have also had mixed results with different manufacturers of Eppendorf tubes. In the end we chose to go with the original as they seemed less prone to contamination in our hands.
Have you tried to use glas vials for the samples... Just to try if the contamination is coming from Eppendorf tubes.
Which solvents do you use in the Eppendorf tubes?
PEG is pretty fairly ubiquitous, and also has many masses since its chain length can vary, and it's hydrophilic. Two things to consider: 1) is the PEG contamination in a mass and retention time range that you're examining for your research question? If not, you may be able to proceed and correct post-hoc. 2) if you think the contamination has to be removed before the analytic chemistry, then i'd try benedikt's approach on a small number to make sure it is indeed from the sample tubes. If your sample is already stored in the PEG contaminated tubes...then you may be out of luck to remove it before the chemistry unless you derivatize it specifically and remove with an extraction.
Just take a moment and think about what you need out of your samples. You have options, and none of them are painless.
Tubes are a common source. There was a paper in Science on this a few of years ago. Its the mold release agents, plasticizers, and clarifying agents that the less reputable (and cheaper) manufacturers add to their tubes to make the manufacturing process cheaper. We had this issue and validated a the virgin PP tubes from Axygen (now Corning) as MS-compatible for these operations. The level varies from lot to lot and even tube to tube within a lot. And, yes, we had to test 400 tubes from each lot ordered to validate each lot. Very painful.
We did something similar to Luke but limited our pain considerably. Only looked at manufacturers, not lots, and max 20 from each. That was about where my pain tolerance said stop. Mad respect Luke!
@luke: Thanks so much. So did you use PP tubes which are 15 ml or which are 1.5 ml for your analysis?
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Atomic, Molecular and Optical Physics
- Atoms