Importing peak boundaries for all raw data file for a molecule viragsagikiss  2020-02-11 12:10
 

Hi all,

I am using Skyline-daily, on Windows 7. Small molecule multi-targeted metabolomics.

First, just want to say how great is Skyline. We are using it for small molecule method development in the last year and I really enjoy both the simplicity the visualisation capability and the flexibility of the software; it is a life saver in many ways.

Now, after put together a multi-targeted LC-MS method to monitor a few hundred compounds in the same time i have run into new questions. I understand maybe not a good idea to bundle up my questions, but if you can help with one of them that's already great!

  1. Peak boundaries! Importing peak boundaries are essential for A; isobaric species (on a QTRAP and TQ in my case) and B; irregular peak shapes (ion-pairing LC)
    After reading through support, i have found this tutorial:
    https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/ImportingIntegrationBoundaries-2_6.pdf

Is there a way to apply Peak boundaries to all Experimental files (*.wiff) in a certain Skyline.sky? or i have to create a "10.000" line csv every time I analyse a new data set?
Also, can i set t1 and t2 to look for the peak only between those parameters? I assumed that's what "Explicit Retention Time Window" does, but regardless what i set there, in case of blanks Skyline picks up peaks minutes away from the RT?

  1. Overlay peaks/anlaytes from the same samples
    to deal with shifty retention time AND/OR isobars, i understand the 'retention time plot' with 'replicate comparison' is almost the same, but for presentation and visualization i still would like to show overlayed chromatograms, do you plan to include this?

  2. Dropbox/Data storage in the cloud [to share data between Skyline Windows/data collection Windows/user's Mac]. Because of the size of the dataset i work on the same *.sky file over the time course of days, leave Windows sleeping, and after continue with the same file I notice some chromatogram disappeared (i.e. Main Window displays 'Chromatogram information unavailable', where used to be data the day before. Same happens time to time when I insert a new transition list (same values, but using molecule list names), or i rename/resave the .sky.
    Do you recommend data is stored in the same folder (or just computer) where Skyline files, or just avoid storing the files in the cloud? Anyone reported similar? I thought i am making a mistake but after this occurred enough times I wonder if it is because all Original Files and Skyline files are in the cloud.

I appreciate the help.
Virag
 
 
Nick Shulman responded:  2020-02-11 14:21
We have some plans to make it so that "Explicit Retention Time" behaves the way that most users expect, where it actually constrains where Skyline looks for a peak, even if no peak is found in that range. We expect this fix to show up in Skyline-Daily probably in a week or two.
This is the page on github where we are discussing the final things that need to happen before the code changes are committed to our codebase:
https://github.com/ProteoWizard/pwiz/pull/633

I think you really would need to have a peak boundaries with duplicated rows in it if you want to set the same peak boundaries on all of the replicates in your Skyline document.

I do not understand what you are talking about in #2. Can you send us a picture?

We might be able to fix the behavior that you are seeing when you use Skyline with DropBox. I will send you an email to find out exactly which files you are looking at and how you are using DropBox and I will see if I can get the problem to happen on my own computer.
-- Nick