Issue 439: MS1 Full-Scan import = match with mascot search, ppm values missing

Assigned To:Guest
Opened:2015-11-17 by alex
Changed:2016-01-06 by Brendan MacLean
Resolved:2015-11-22 by Brendan MacLean
Resolution:Not Repro
Closed:2016-01-06 by Brendan MacLean
2015-11-17 alex
Title»MS1 Full-Scan import = match with mascot search, ppm values missing
Assigned To»Brendan MacLean
Hello Brendan,

I am using skyline-daily (64-bit) and encountered some missing information when importing MS1 information.

I got the .dat file from mascot & the .raw file from the MS/MS (I also tried the corresponding profile mzXML file). I do see the MS/MS spectra and the MS1, MS1+H, MS1+2H ion chromatograms, peak boundaries and the black triangle indicating the correct peak group.

What I don't have: the vertical red line with ID showing at which time the MS/MS spectrum was taken.
What I don't have: the ppm per peak group (although selected in the legend menu, right mouse click).

I attached the file in question here. I hope its just a check box I did not click, but the ppm values should really show up when toggling the menu, shouldn't they?

All the best,

2015-11-22 Brendan MacLean
resolve as Not Repro
Hi Alex,
I would prefer that you start these on the support board, unless you are positive that your issue represents a bug in Skyline and you have clear steps to reproduce it.

In this case, when I open the file you include, I can see perfectly well, both the ID annotations and the PPM mass error values. So, I must assume that you have somehow turned them off in your Skyline instance (this state gets saved to your local settings, but not the document). To turn these UI elements back on, you must right-click in the chromatogram graph, and then make sure "Mass Error" is checked and "Peptide ID Times > Matching" is also checked.

Hope this helps. If not, we may need to WebEx or Skype for me to understand what is going on with your system.


2016-01-06 Brendan MacLean
Assigned ToBrendan MacLean»Guest