We just use peptide lists and don't care about protein associations.
One thing though is that we really care about individual peptides even if they have some problematic characteristics.
It took me some time to reproduce of few things I encountered.
We are using heavy reference peptides for our assays.
Due to the irregularity of our peptides we would receive them with a single heavy AA at a specified location in the peptide.
Note the presence of a heavy L as well as a light L.
If I paste this into skyline I will not get any variable modifications (like M[+16]) applied.
This is in contrast to pasting PEMPLTIDLME.
It's clear to me why that is the case but the result is that I have to generate all variable modifications externally and paste it like so:
A workflow for peptide import where skyline just does this would be great of course.
Also I wanted to look into the collisional dissociation of our peptides in detail.
For this I activated neutral losses for loss of water and amonia loss.
When I then imported my peptides I would get countless duplicated transitions.
I have attached an example skyline file for this (neutral_loss_issue).
In this file there is for example 4 times: L [y8 -51.1] - 891.4822+
Importing results with this would then yield eg:
Duplicate transition 'L - y8+' found for peak areas
Of course these transitions are not really unique in a strict sense but it would be great is this was handled more gracefully.
The issue was created by just pasting the string "ALNEKLVNL" into the empty target list of the example file.
Also, if you open the example file, go to peptide settings, and disable the structural modification for water loss, you will trigger:
An item with the same key has already been added.
We are using a Q Exactive and thermo seems to encourage the use of normalized collision energy.
When I try to do collision energy optimization with normalized energies, skyline would import the .raw file but would not recognize that the various spectra are based on different collision energies.
I am using Skyline 126.96.36.19905.
These are some of the things that I would love to have some help with.
Best wishes for a happy new year,