Need Cmdline runner commands for the following. kartik kundgol  2019-07-15

Hi Team,

We need Skyline Command Runner commands to refine the MRM transitions based on the following criteria:

  1. To identify RT of each peptide by looking for signal from multiple charge states for the same peptide overlaid.
  2. To identify the most intense precursors for each peptide.
  3. To identify a, b, y, z ions
  4. To rank orders each MRM/precursor charge state/peptide.( Selection of the top 2-3 MRM’s/ charge state/peptide for collision energy optimization.)
  5. To pick the best collision energy values for each MRM transition


Brendan MacLean responded:  2019-07-16

Hi Kartik,
Hard to tell exactly what you are asking for. Are these things you know how to achieve through the Skyline UI, which you need access to through the command-line, or are you requesting entirely new features?

When I read the requests, some seem possible to me with the command line and a custom report that outputs the values you are seeking. Are you already using Skyline command-line successfully for other things?

Maybe start by detailing how you get what you want from the Skyline UI and how you imagine getting it through the command-line.

Thanks for your feedback.