MS or MS/MS scan numbers

MS or MS/MS scan numbers mvillal1  2019-03-19

Hello Skyline team,

Is there a way to extract/show on the Document Grid the MS or MS/MS scan numbers per precursor?


Nick Shulman responded:  2019-03-19
If you want to know the number of scans that occurred between the start and end of the peak, there is a number available on the "Transition Result" called "Points Across Peak".

If you want to know what the actual scan numbers are, there is no way to get that information out of the Document Grid at the moment.
You can get the retention times or intensities of the chromatogram from the Document Grid. Those values are available under the "Chromatogram" thing under the "Transition Result" when you are editing a view in the Document Grid. Currently there are no scan numbers there, but I could certainly add that if it would be useful for you.

I am not sure I understand what you are asking for.
-- Nick
mvillal1 responded:  2019-03-19
Hello Nick,

The actual scan numbers, sorry for the confusion. The numbers that you can see on the MS or MS/MS spectrum (i.e., 0.1.21230... similar to those reported by SeeMS).

Nick Shulman responded:  2019-03-19
It would be straightforward to provide the list of scan numbers in the document grid.
They would be under:
Proteins > Peptides > Precursors > Transitions > Chromatogram > Raw Data
It would be a comma-separated list of all of the scan identifiers that contributed to the chromatogram.

A scan identifier is usually a bunch of numbers separated by dots, such as "0.1.6126". The different mass spec vendors have different ideas about what the things in between those dots mean.

Would something like this be useful to you? Are you writing a program that will do something with these numbers?
-- Nick
mvillal1 responded:  2019-03-20
Hello Nick, thanks for the reply.

Yes, actually, I started looking for scan numbers under Chromatogram --> Raw Data in the edit view option. It will be useful for our lab as we are bench-marking peptide de-novo software approaches to MS1 extractions with Skyline and identifications from other database driven approaches. I don't know how difficult this will be to implement. I have also seen some old posts in the support forum asking for scan numbers to be extracted from Skyline... so perhaps other groups can benefit from this?