Issue 1004: Add support for adding modifications from the command-line

Status:open
Assigned To:Brendan MacLean
Type:Todo
Area:Skyline
Priority:2
Milestone:23.2
Opened:2024-01-25 09:07 by Brendan MacLean
Changed:2024-01-31 08:09 by Brendan MacLean
Resolved:
Resolution:
Closed:
2024-01-25 09:07 Brendan MacLean
Title»Add support for adding modifications from the command-line
Assigned To»Matt Chambers
Type»Defect
Area»Skyline
Priority»3
Milestone»23.2
FragPipe team has requested support for defining peptide modifications in Skyline through the command-line. Seems like an obvious next addition to your command-line settings support which initially focused almost entirely on transition settings.

2024-01-25 09:10 Brendan MacLean
Notify»fcyu
TypeDefect»Todo
Priority3»2

2024-01-30 13:36 Matt Chambers
Brendan, the "import-search-add-mods" option tells Skyline to accept all mods from the search. Is this issue referring to only accepting the specified mods, or is it referring to adding/removing mods from the document settings?

2024-01-31 08:04 Brendan MacLean
resolve as Fixed
Statusopen»resolved
Assigned ToMatt Chambers»Brendan MacLean
This is more fine-grained direct adding of modifications, 1-by-1, definitely should make it possible to add by Unimod ID or SCIEX short-name, and of course the full Matrix Science long name we use... and also giving the full definition of a modification.

This will give users more control of what gets added to the document rather than just accepting everything we guess from the search results. Our guesses are not always 100% correct and a user may only care about certain modifications from the search.

2024-01-31 08:09 Brendan MacLean
reopen
Statusresolved»open
Wasn't intending to resolve it.