• Sign In
  1. Requests

Skyline Command Line Help

support

View Request

view list print
Skyline Command Line Help anirudhkashyap511  2024-07-22 12:18
 

Dear Skyline Support Team,

I hope this message finds you well. I'm reaching out to seek guidance on two specific features within the Skyline command-line interface:

  1. Removing Empty Proteins: Is there a command-line equivalent for the "Refine -> Remove Empty Proteins" function available in the GUI?
  2. Missed Cleavages Not Appearing: Despite setting --pep-max-missed-cleavages=0, I am noticing that some peptides which do not associate with the provided FASTA file but have a spectral library match still appear in my results. Here is the command I've been using:

%SKYLINE_CMD% --in=%INPUT_SKY_FILE% --import-search-file=%LIBRARY_PATH% --import-pep-list=%PEPTIDE_LIST% --pep-max-missed-cleavages=0 --associate-proteins-fasta=%FASTA_FILE% --refine-auto-select-transitions --refine-missing-library --refine-auto-select-peptides --save --out=%OUTPUT_FILE%

Attaching an image for better reference
 
 
Nick Shulman responded:  2024-07-22 13:02
Can you send us your files so that we can reproduce that command line that you are running?

I guess we would need your peptide search results, your starting Skyline document, the file with the list of peptides you are specifying with that "--import-pep-list" and your fasta file.

Files which are less than 50MB can be attached to these support requests. Alternatively, you could zip everything up and upload it here:
https://skyline.ms/files.url

Note that if the peptides in the "--import-pep-list" file have missed cleavages, they would end up getting added to your document regardless of the "pep-max-missed-cleavages" setting. Typically when you ask Skyline to add a particular peptide the peptide will be added regardless of whether other settings would normally prevent the peptide from being added.

I believe the way to achieve the same thing as "Remove Empty Proteins" is to specify "--refine-min-peptides=1".
-- Nick
 
anirudhkashyap511 responded:  2024-07-22 13:31
Hi, thank you for "--refine-min-peptides=1". Its working.

However, the missed cleavages question, it does exist in the peptide list. (The missed cleavage) but in my template skyline file, i haven't allowed any missed cleavages. And there are a lot of missed cleavages (if im not wrong) but only one stray peptide appears in the list. Attaching all the files that I used in my batch script.

%SKYLINE_CMD% --in=%INPUT_SKY_FILE% --import-search-file=%LIBRARY_PATH% --import-pep-list=%PEPTIDE_LIST% --pep-max-missed-cleavages=0 --associate-proteins-fasta=%FASTA_FILE% --refine-auto-select-transitions --refine-missing-library --refine-min-peptides=1 --save --out=%OUTPUT_FILE%


This is the command I used.