Issue 550: Only iRT traces are imported

issues
Status:resolved
Assigned To:Brendan MacLean
Type:Defect
Area:Skyline
Priority:3
Milestone: 
Opened:2017-10-03 by an.staes
Changed:2019-10-04 by Nick Shulman
Resolved:2019-10-04 by Nick Shulman
Resolution:Fixed
Closed:
2017-10-03 an.staes
Title»Only iRT traces are imported
Assigned ToGuest»Brendan MacLean
Type»Defect
Area»Skyline
Priority»3
Milestone»4.1
Dear,

When trying to import some SRM raw files from TSQ Vantage, the only signals that are imported are the iRTs. The rest of the peptides are not imported. I did a set of peptides split in 4 subsets. For the first subset (1-1), the signals are shown, but for the 3 others subsets, no signal is seen for the monitored peptides. In Xcalibur all signals are there, so I don't know what is wrong. I tried to rerun the methods, ,but it had the same effect... All methods are the same, except for the set of peptides monitored....
I attached the skyline file. The raw files are to big to attach.
Can you help me out on this?

Thank you for looking into this problem!

I'm using skyline Daily version 3.7.1.11357

Best,
An
 
 Salm_All_invitro_splitMeth_70min_171003_flatgradMiddle.sky.zip

2017-10-03 Brendan MacLean
Assigned ToBrendan MacLean»Kaipo
Notify»Nick Shulman;Brendan MacLean
We need some kind of warning about this. It happened to me also, and it took too long for me to notice. I imported 46 replicates and completely missed that one had an iRT alignment failure and didn't import any other chromatograms. In my case, as in the one Nick pointed to, I wasn't even using the iRT prediction to determine the retention time windows. It was DDA data with "Include scans withing minutes of IDs". So, it was really silly to have the failure discard the chromatograms. I guess that is two bugs. I will look at fixing the discarding when the alignment is not used in extraction.

Kaipo, can you look at the error/warning when iRT alignment fails.

An, that is the problem. We import the iRT chromatograms to allow you to diagnose the iRT alignment failure, instead of just causing an error, which would cause all chromatogram for the file to be removed.

2019-09-15 Brendan MacLean
Assigned ToKaipo»Nick Shulman
NotifyNick Shulman;Brendan MacLean»
Milestone4.1»
You worked on this one, right? Is it good enough to resolve?

2019-10-04 Nick Shulman
resolve as Fixed
Statusopen»resolved
Assigned ToNick Shulman»Brendan MacLean
I think we deal with this correctly in Skyline 19.1:
1. We only stop importing chromatograms if the Transition Settings Full Scan Retention Time Filter is "scheduling windows".
2. If we stop importing chromatograms, we show the error message "Unable to finish importing chromatograms because the retention time predictor linear regression failed."
(This work was committed on May 24).