A protein sequence cannot contain the character 'z' at line 230 nicrdo  2022-03-07


I am new in the Skyline heaven and I am trying to set up a PRM method.

Unfortunately, in one of the first step i can not load the proteome of Pseudomonas putida.

The error message is the following.

Is there any way to solve this?


Nick Shulman responded:  2022-03-07
It looks like you are trying to use a FASTA file whose name ends in ".gz".
".gz" normally indicates that the file has been compressed, and you will need to uncompress that file before you can use it in Skyline.

I am not sure whether Windows natively knows how to uncompress .gz files. It might be that you will need to install something like "7-zip" (from here: https://www.7-zip.org/ ) and after you have done that you will be able to right-click on the file in Windows explorer and tell 7-zip to uncompress it.
Then you will be able to tell Skyline to import the FASTA file "pputidaproteome.fasta" (without the .gz on the end of its name).

-- Nick
nicrdo responded:  2022-03-07
Thank you so much Nick! Yes, the problem was that the file was compressed. I have uncompressed it and now it works. Thank you for your help! Have a wonderful day.