I want to do LC–MS analysis of the samples from a 384-well plate where each compound (at around 1–10 μM) is dissolved in 10–15 μL of DMSO. I am worried about the DMSO dwarfing the analyte’s signal, as well as the challenges from ion suppression caused by the DMSO.

So, I’d like to evaporate DMSO and replace it with something like ethanol/water (1:1) before passing it on to my autosampler. Does anyone have any experience doing this? The DMSO removal protocols I found are suited for removing a much larger quantity from a single sample.

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    $\begingroup$ Have you tried to dilute-and-shoot? Could you share additional information about the analyte and MS? Do you know why DMSO was chosen in the first place and whether it can be replaced with something else in the future shall there be more samples? I presume it might a biological extract with DMSO used as cryoprotectant. Also, do you have access to a high-performance freeze-dryer? Freeze-drying DMSO is a pain, but for small quantities like this it might be worth considering (check out volatility of analyte). $\endgroup$
    – andselisk
    Jul 16, 2023 at 8:25
  • $\begingroup$ These samples were generated from some colleagues' internal HTS libraries that they had in the back of their freezer, so are all small drug-like compounds -- some solo compounds, some in mixtures. This is in the planning phase so we haven't actually tried the dilute-and-shoot yet. The compounds of interest are going to be around 100nM. $\endgroup$
    – Eric J
    Jul 17, 2023 at 10:00
  • $\begingroup$ Why not just rely on chromatography to separate the analytes from the DMSO? Sure, there might be a huge DMSO peak in your chromatogram, but DMSO isn't retained all that well on C18 chromatography resins. If most of your analytes are more hydrophobic than DMSO they should be separable from the DMSO during chromatography. If so, then DMSO won't lead to ion suppression. $\endgroup$
    – Curt F.
    Jul 17, 2023 at 14:59
  • $\begingroup$ If you have 10 mM solutions, after 100x dilutions you still have 100 uM. If you inject 1 uL of that dilution, it's still 100 pmol on-column. Should be easily detectable by any decent LC-MS setup. $\endgroup$
    – Curt F.
    Jul 20, 2023 at 0:49

1 Answer 1


The standard way to remove water and replace with volatile solvents for microscopy is with a dehydration series, e.g., replacing water with ethanol, and then ethanol with acetone. To more thoroughly remove solvents, critical point drying is used, which should greatly reduce the DMSO in the sample, leaving $\ce{CO2}$. However, if you're analyzing volatile components, then this would badly change the sample!

If there is a microscopy lab at your institution, you might try to use some of their apparatus for dehydration.

However, rather than put valued samples though the treatment, first make a control sample, with known chemicals plus DMSO solvent, and evaluate via LCMS before and after the drying treatment to see how effective drying is and if it is even needed.

  • $\begingroup$ I'm afraid using dehydration series could result in even greater substance and, consequently, signal loss that that from DMSO the suppressor. I'm not sure how to use critical point drying for the well plate and not to face a carry-over or cross-contamination problem. Are there any models suited to use with well plates, especially with the larger ones that OP is using (384 wells)? $\endgroup$
    – andselisk
    Jul 16, 2023 at 8:32

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