Command Line Enhancement Request : Include MS/MS Filtering Options

Command Line Enhancement Request : Include MS/MS Filtering Options philip remes  2022-09-21 18:17

Hi guys,

The command line documentation lists some options for MS1 filtering that can be changed, under the Document Settings. What do you think about adding the MS/MS filtering options? These are: Acquisition Method, Product mass analyzer, Resolution, and even Isolation Scheme for the DIA acquisition method. A work around could be for an application to store Skyline file templates with the desired settings, but this is not as flexible as programmatic access.


Brian Pratt responded:  2022-09-28 09:15

Hi Philip,

There are an awful lot of Skyline settings that could be exposed on the commandline, we've prioritized those that are likely to change from job to job. Of course "likely" depends on what kind of jobs users are into, which is a boundless field, so this kind of feedback is useful.

Skyline itself is, of course, the application for creating templates with desired settings, but it sounds like you maybe have an application where you need to be able to adjust MS/MS filtering in realtime?

Best regards,

Brian Pratt

philip remes responded:  2022-09-28 09:52

Hi Brian,

I understand you have to make prioritizations. For me, these listed ones would be useful to change, in particular the Acquisition Method, however using skyline files as templates is a viable solution for most parameters. The real-time changing of parameters comes into play with the Isolation Scheme: I have files that I'd like to import with the DIA mode, but not all the MS2 acquisitions in the file should be imported. So it would be nice for the application to detect which ones to import, and create the appropriate Isolation Scheme.


Brian Pratt responded:  2022-09-28 12:18

I'll add to this to our development queue. No promises as to timeline, though!

Best regards,