• Sign In
  1. Requests

Transitions not found in results files

support

View Request

view list print
Transitions not found in results files as3e15  2018-02-19 03:21
 
Dear Skyline team,

I am encountering a problem that i cant seem to find help for in your support section. I am doing an MRM experiment but it seems when i import my results files, some of the transitions have no data. I know this is not the case because some other runs (of exactly the same thing, in exactly the same conditions) have data for these transitions. to be more specific, it seems to be the precursors of every peptide which does not show up.

I am using a Waters Synapt G2-Si mass spectrometer.

I have attached a screenshot of what i mean.

I hope i have made this clear and given enough information for you to help.

Many thanks,

Andy
 
 
Nick Shulman responded:  2018-02-19 12:15
Is it possible that you really do not have any MS1 scans in that particular replicate?

Another thing that could prevent you from getting chromatograms for your precursors would be if your settings on:
Settings > Transition Settings > Full Scan
had "Isotope Peaks Included" set to "None".
However, this is unlikely to be the problem for you since your other replicates seem to have peak areas for those precursors.

It might help if you sent us your files.

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including extracted chromatograms.

You can upload that .zip file here:
https://skyline.ms/files.url

You should also send us that your raw file for that problematic replicate.
 
Brendan MacLean responded:  2018-02-19 12:53
Another possible explanation is that you imported the run you are showing before you added the precursor targets to your document and then the other runs after you added them. Skyline requires a re-import (Edit > Manage Results - Re-import) to extract new chromatograms. Otherwise, it will leave targets showing just the chromatograms extracted for the original import.

So, if you had MS1 filtering turned off and imported a file and then turned on MS1 filtering and imported another file, you would end up with a document like the one you are showing.
 
Brendan MacLean responded:  2018-02-19 13:06
Alternatively, since you did not include a screenshot of your Transition Settings - Full-Scan tab it may be that MS1 filtering was on for the original files imported and got turned off before this most recent import, which would also cause what you are seeing. If the replicates you are showing are ordered as they were imported (as opposed to Acquired Time ordering) then this would have to be the order of events, since the replicate missing precursor chromatograms appears last in the order.
 
as3e15 responded:  2018-02-20 07:31
Dear Brendan and Nick,

Thank you for the quick responses. I re-visited my MS/MRM method on mass lynx for the synapt G2-Si and it turns out the RADAR setting had been turned off, therefore there was no full scan being done and as such i presume this is the reason i am seeing no MS1 data. Perhaps this may help anyone in the future if they come across the same issue.

I am very sorry to have wasted your time but i must commend you on your consumer support. Skyline is a great piece of software and the team behind it makes it even better.

Many thanks,

Andy