Issue 544: Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges

Assigned To:Guest
Opened:2017-09-21 by robwsprung
Changed:2017-12-19 by Brendan MacLean
Resolved:2017-12-19 by Brendan MacLean
Closed:2017-12-19 by Brendan MacLean
2017-09-21 robwsprung
Title»Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges
Assigned ToGuest»Brendan MacLean
Hi Brendan,

This issue is in response to issue 539, which I am unable to update with a response.

To reiterate, I am importing DDA data to determine the retention times when my precursors of interest elute. Although I have my Transition Settings set to "Include all matching scans", data is not imported across the entire chromatographic range. Sometimes this results in the peak of interest not being displayed, or being truncated in one of the channels.

I have uploaded a Powerpoint file containing screenshots to the File Sharing directory as I am unable to upload it to the board.
(Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges.pptx)


2017-09-21 Brendan MacLean
Hi Robert,
If you are unable to update these requests, this may not be the best place for this discussion, as I am not exactly sure how you will respond to me. Maybe it would be better to use the support board, and I can post to the issues list once I understand the issue and that a code change in Skyline is needed. I would expect you to have an easier time attaching a powerpoint file to a support request also. I have attached your file to this response.

Okay, this does look like a problem that requires a code fix. Is this new in Skyline-daily, or do you see the same issue in the Skyline 3.7 release?

Are you extracting any fragment ion chromatograms at all?

We recently changed Skyline to reduce MS1 chromatograms to the range of MS/MS chromatograms if they are present, which is an important improvement for PRM, but even so, I would agree that this should be done at the peptide level and not the precursor level. So, that all precursors for the same peptide have the same chromatogram range.

I am sure we can get this fixed to meet your needs. I just need to understand the context a bit better.

Thanks for posting the issue and providing the screenshots.

 Discrepancies in Heavy and Light Peptide Chromatogram Import Ranges.pptx

2017-12-19 Brendan MacLean
resolve as Fixed
I believe Nick has fixed this.

2017-12-19 Brendan MacLean
Assigned ToBrendan MacLean»Guest