Thank you for sending those files.
When I look at "AK_10.d" in ProteoWizard SeeMS.exe, I see that the spectrum at 37.82495 minutes really does say that its total ion current is NaN ("not a number").
Do you have any idea why the value is that way?

I tried converting the .d file to .mzML, and that spectrum did not appear in the .mzML file: it skipped right from 37.8039 to 37.846.

We could fix this so that Skyline skips over NaN values when calculating the TIC, but it might be that there is some other problem with AK_10.d that we should not be ignoring.
-- Nick

Hi Nick,

That's interesting. Now that I look more closely at the TIC chromatogram, there is a gap in the 37.8 minutes where it just disappears. I checked a few of the other samples and it does seem like the TIC drops off for a fraction of a minute in the NaN ones, while I didn't find that in the good ones. I then looked at these files in Agilent's IM-MS Browser software, and the TIC is briefly dropping to zero in those chromatograms as well.

I've asked around and we haven't seen this issue before in our group, but our best guess is that something in the electronics of the instrument just didn't collect for that frame. Seems like it would be useful to have a workaround to skip over NaN values, at least for these samples. But, I'm not really sure if this would ever be indicative of a bigger problem, and am not sure if that would be a good general rule to apply.

I'm attaching another few .d files in case it's helpful. AK_02 and 03 had the TIC area NaN (thanks for defining this acronym for me!). 01 and 04 were good.

Thanks for your help!
Anna