Simon,

I will try to add a column to the Document Grid which will tell you this number.

Can you send me one of your Skyline documents with some proteins and peptides in it? With new features like this, it's always good for us to be able to see some real world data where the feature is going to be used, so we can make sure that the feature looks right.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing the Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url

By the way, do you know what we're supposed to do if the protein sequence has repeats in it, so that a particular peptide sequence can be found in more than one location in the protein sequence? My guess would be the peptide would get counted twice so that the % coverage is telling you the number of amino acids in the protein sequence which could belong to a peptide in the document. But, I could also imagine that the community might already have chosen a different convention as to what to do in this case.

-- Nick

Dear Nick

thank you for your response.
You can find the Skyline documents attached.
The MS data quality is not very good because we are just starting with proteomics workflows at our research group but for that purpose it should be sufficient.

Considering your question I am not sure. In my opinion I would assume each peptide repeat is included in the calculation of the sequence coverage.

Cheers,
Simon

Thanks for sending your file. The new "Protein Sequence Coverage" column will appear in the next update of Skyline-Daily.

Here are a couple of screenshots of what the feature will look like.

Let me know if you can think of anything that should be changed.
-- Nick

Thank you for the fast and competent support.

It looks great.

I am looking forward for the next update.

Cheers,
Simon

Hello,

I am a new user of the skyline and also coming across a similar issue. I also need % sequence coverage for the analysis that I am trying to perform. I tried to follow the steps with reference to the screenshots attached in the above communication but unable to find the %sequence coverage option.

Is it exclusive for specific users? What can I do if I want to avail this facility?

I also wanted to know if there is any possibility of method automation with Skyline. I am currently using the Shimadzu QTOF system for glycoprotein characterization. I need to get multiple sets of information such as %sequence coverage, digestion efficiency, post-translational modifications, etc.

Can someone please guide me if it is possible with Skyline?

Many thanks in advance.

Regards,
Amita

Amita,
The % sequence coverage column is a new feature which first became available in the Skyline-Daily that was released this morning.

There is a button to download "Skyline-daily (beta)" on the main Skyline page:
https://skyline.ms/project/home/software/Skyline/begin.view

What exactly do you mean by "method automation"?
It has always been possible to control Skyline from the command-line and right now we are working on a new tool called "Skyline Batch" which will make writing scripts for Skyline's command-line easier.

You can learn more about Skyline batch here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=skyline-batch

-- Nick