We have an abundant contaminant in our MS results (Q-Exactive Plus).
Like PEG, it has hundreds of instances in each run, each instance with a different parent mass and several charge states.
Many of the instances share dominant MS/MS peak masses, including the singly charged peaks at 123.117, 202.107 and 216.123 Da, and more.
Examples of singly charged precursor masses are 996.598, 1051.717 and 1334.893.
Any idea about the identity of this contaminant?
Thanks,
Ilan
You might check for algal growth in an aqueous phase especially if you keep using the same reservoirs without thoroughly cleaning them. Algae and molds can cause contamination with large molecules such as you observe. Clean glassware is evenly wet by water, if this is not the case the glassware is too dirty to be used for mass spec. These peaks might also be the sodium and potassium adducts of polyethylene glycols. I have seen contaminants like this from the adhesive on lab tape someone used to label the solvent lines or secure the tops on the reservoirs on the HPLC. Did you use Parafilm on or near the solvents? This could also be the source of the polyethylene glycols. Never use sealing tape like Parafilm on or near the reservoir bottles or solvent lines on any LC/MS system because this type of contamination is possible. If you need to cover the reservoirs use aluminum foil with the dull side facing the solvent.
I would suggest trying those masses at MaConDa:http://www.maconda.bham.ac.uk/search.php and http://www.pennstatehershey.org/web/core/contaminants to make sure that they are not very common ones! Good luck, Biswa
Hi Ilan,
Please send me a screen shot of the chromatogram. I need to see the elution time. Pleae send it to my email, I don't come here so often.....
Michal
Hi Ilan,
Hard to say. It could be helpful to know the retention times - do these compounds elute early, late, together? Do you see them in all samples, even in blank ones? Did you try replacing the HPLC solvents and bottles? Are the precursor mass differences equidistant? Could you please upload a HCD spectrum of one of the compounds?
Best wishes,
Christian
Hi Christian,
The major contaminants of this type elute relatively early – before minute 100 (in our program, peptides elute between 40-160 minutes). The contaminant peaks are dense in this area and almost disappear afterwards. The major contaminated m/z range is 300-450.
I can't see regularity as in PEG.
I don't think that the problem is in the HPLC because another user of the MS facility does not have this contaminant.
An MS/MS spectrum is now attached to the original post.
Best regards,
Ilan
Hi Ilan,
Thank you for answering my questions and apologies for the late answer. You wrote that the majority of peaks is in the m/z range 300 to 450. Could you please also let us know what the mass range is? It puzzles me (an I guess you as well) that there is no regularity in the parent masses. The product ion spectra are also pretty rich. You said you see common product ions for most of these impurities, indicating that they belong to the same substance class or share the same groups. I was wondering whether these molecules are actually peptides that possess some kind of modification. Have you tried a “blind PTM” search – just to exclude this possibility? I would also suggest to check for typical immonium ions if you have not already done so. Honestly, I do not have any other good idea, most other substance classes crossing my mind would either not show these retention times or dissociate very differently or are just unlikely to be found as impurities in your samples. Have you tried calculating the elemental composition for some of the molecules with lower masses?
Best wishes,
Christian
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