Batch import custom annotation settings and tracking chromatogram corrections.

Batch import custom annotation settings and tracking chromatogram corrections. velasqe2  2019-09-12

I had two questions, one regarding custom annotations and the other regarding peak editing.

  1. Is there a way to import a batch of custom annotations at a time. Currently the user has to add annotations to the protein environment one at a time through document settings but we were wondering if there is a way to pre-define custom annotations and import those settings into document settings.

  2. Is there a way to track the process of peak editing that a user might perform on certain chromatograms? and if so, can we export the editing process as a csv that holds all that information?

Any advice helps, thank you all!

Nick Shulman responded:  2019-09-12
Import Annotations:

In Skyline there is a menu item:
File > Import > Annotations
which lets you import a list of annotations and other built-in properties from a CSV file.

You should use the menu item:
File > Export > Annotations
to see the complete list of properties that can be imported and also to see what the format of the CSV file should be.

Tracking Peak Editing:

Skyline has an "Audit Log" which will show you all of the edits that a user has made to a Skyline document. You can get to it with the menu item:
View > Other Grids > Audit Log

If you just want a list of all of the peaks that have been manually adjusted, and you don't care about what order all of these changes were made in, you can use the Document Grid. There is a column called "User Set Total" on the "Precursor Result" which tells you whether a user manually adjusted the peak boundaries.
If you want to learn more about the Document Grid you can take a look at the Custom Reports tutorial:

-- Nick
velasqe2 responded:  2019-09-12
Hi Nick thank you for your response!

I figured out how to import and export custom annotations but my question is really about setting up the annotations in document settings. Settings> Document Settings>Add... Whenever I want to create a new field for a custom annotation I have to manually add each one. Is there a way to add a bunch of new fields at the same time (including the type of annotation and at what level it should be considered)?

Thank you for the tracking peak editing part I will try it out!

Nick Shulman responded:  2019-09-12
No, there is no way to define a bunch of annotations as a batch.
We recommend that you start with a Skyline document that already has the necessary annotations defined in it.

By the way, if you find that you are defining many annotations on things like your replicates, then I recommend that you take a look at the relatively new feature called "Lists".
Here is some information about Skyline lists:

Unfortunately, there isn't a batch way to define lists either. We have not received much feedback on the lists feature yet, so I am not exactly sure how people are going to end up using them.
-- Nick
velasqe2 responded:  2019-09-12
Thank you I appreciate the advice and help!