Running peptide search with MsAmanda from commandline

Running peptide search with MsAmanda from commandline fcsigloch  2021-05-12

I am using Skyline form commandline (using SkylineCMD.exe). So far, I performed the peptide search with MSGF+. Now I would like to switch to MsAmanda. Can I run it directly from the Skyline executive or do I have to run the search separately?
I could not find an appropriate command in the CLI documentation.
Greetings, Florian

fcsigloch responded:  2021-05-12

By the way, I found an inconsistency in the CLI documentation: I believe the commands for the full scan product resolution and the corresponding mz is given incorrectly in the PDF.
I guess those should be similar to the precursors, i.e.:
-- full-scan-product-res=<resolving power> instead of "--full-scan-product_res=<resolving power>"
--full-scan-product-res-mz=<m/z value> instead of "--full-scan-precursor-res-mz ==<m/z"

Brendan MacLean responded:  2021-05-12

Hi Florian,
We have not yet implemented our own MS Amada interface through the Skyline CLI.

Good eye in the documentation, but you should be using Help > Documentation > Command Line inside Skyline or --help with SkylineCmd.exe, which is the most current CLI documentation and built with safeguards that should keep it from ever having a problem like that.

If you look again on this page:

You will see the PDF version has been deprecated:

NOTE: for the most current command-line documentation, run SkylineRunner.exe or SkylineCmd.exe without any command-line arguments. The same information can be found in the Skyline user interface at Help > Documentation > Command Line.

I just added strikethrough text to hopefully dissuade more people from continuing to refer to this documentation for any version with the newer documentation built in.

Thanks for your feedback.