saving all transition image files at once and adjusting based on y-axis for selected peak jiwon hong  2021-07-20

Hello Skyline team,

My name is Jiwon and I am currently a graduate student at Korea University.

I have been using skyline for a few months, but couldn't find a solution for a very time consuming/repetitive job which lead me here.

I wish to save the image files of the transitions: 3 files (total, light, and heavy) for each peptide with a specific pattern name.
For peptide sequence XXXX,
I wish to save the total image file as XXXX_a, light as XXXX_e and heavy as XXXX_s in a designated directory (they can all be in the same directory) in .jpg format.

Currently, I was only able to save the files through right clicking > Save image as one by one, and was wondering if skyline is capable of saving all the images at once.

And also, would it be possible to leave the x-axis and only auto adjust the y-axis based on the selected region only?
An example file is attached below (skyline_adj : wanted scale, skyline_no adj: default image)

Thank you in advance!

Jiwon Hong

Brendan MacLean responded:  2021-07-21

For this sort of thing, we would generally recommend that you upload your document to and then interact with the web interface there.

There are whole other website interfaces built on top of querying for images and data. For instance, the CPTAC Assay Portal:

Hope this helps. We have not implemented any sort of programmatic access to the plots in Skyline itself.