I am trying use the "Copy Data" feature to copy the data from the "Full Scan" viewer that appears when you click on a chromotagram.

In general I think it is really useful to extract the underlying data from the visualizations in Skyline, however I am finding the way the output is formatted difficult to understand. What I would like to do is plot the data from the scan in R, but the format makes that difficult without moving a lot of things manually. At this point I am questioning whether the formatting is a feature or a bug.

I'm pretty sure the "Copy Data" feature is simply broken for scans with ion mobility data. I've attached a csv with the output that I am seeing when copying the data from a scan from a timsTOF .d file. The columns for m/z and 1/K0 (Vs/cm^2) are repeated multiple times. It looks like the values for intensity are there but it not clear which rows they apply to. In row 3, 1/K0 (Vs/cm^2) is repeated in 57 columns.

I would think the best way to format the output would be a simple table with a single header and 3 columns: m/z, 1/K0 (Vs/cm^2), and intensity.

The first thing I tried to do was to see what the output for a 2D scan without ion mobility data looks like. I think it a bit more comprehensible but still not very R/python friendly. There are 3 separate set of headers for each ion annotation.

Again I would think the best format would be a simple table with 3 columns: m/z, intensity, annotation.

Thanks,

Aaron Maurais