Proteomics data processing into sample vs protein intensity matrices

Proteomics data processing into sample vs protein intensity matrices saharak  2020-07-19


I am interested in downloading and processing proteomics data into sample vs protein intensity matrices for various disease types that include healthy control samples.

For the datasets that have been processed with skyline, I found that there is a viewer for windows, however, I wasn’t able to find any library to parse them. How do you recommend that I process them into sample vs protein intensity matrices?

I also found "MSstats" package::SkylinetoMSstatsFormat and lipidr::read_skyline, however both require sky csv files and I am only able to download .sky file. Where can I find the csv format and if I can't directly download it, how do I process the .sky files into csv files?

Also, where would I be able to obtain information on each sample, e.g. whether diseased or normal?

Thank you

Nick Shulman responded:  2020-07-19
If you want to get lists of numbers (for instance, as a .csv file) out of a Skyline document you should use the "Reports" feature.

Here is a tutorial which shows how to create a custom report to get data out of Skyline:

We have not written any libraries that make it easy to read Skyline's file formats. There is a way to invoke Skyline from the command line if you need to, for instance, tell Skyline to export reports from a large number of Skyline documents. You can find information about the Skyline command line using the menu item:
Help > Documentation > Command Line

If you want to see how to use Skyline and MSstats to compare values from healthy and diseased samples, you should look at the Grouped Study Data Processing tutorial:

-- Nick
saharak responded:  2020-07-20
Thank you Nick.
It seems that the skyline application can only be installed on a windows computer. Is there any other alternative for macOS to generate sample vs protein intensity matrices?
andyzcq responded:  2020-07-23
Hi, saharak

Skyline can output the precursor ion intensities, and then you can use InfernoRDN software to transform the precursor ions into protein intensities by summing top three peptide intensities.

You can download InfernoRDN at

Hope it helps.