Issue 817: Small molecule support for Import > Transition > List column picker

issues
Status:open
Assigned To:Brian Pratt
Type:Todo
Area:Skyline
Priority:1
Milestone:21.2
Opened:2021-06-12 by Brendan MacLean
Changed:2021-06-12 by Brendan MacLean
Resolved:
Resolution:
Related:766
Closed:
Related Issues
2021-06-12 Brendan MacLean
Title»Small molecule support for Import > Transition > List column picker
Assigned To»Brian Pratt
Type»Todo
Area»Skyline
Priority»1
Milestone»21.2
Related»766
This really should happen for 21.2. The File > Insert > Transition List form with customizable columns turns out to be too confusing to teach in real-time. It requires the user to inspect a spreadsheet and replicate its column layout in the form grid, which is not something a class of 25-50 people can do reliably enough for it not to derail the session. We have moved to relying instead on using spreadsheets will perfectly named columns so that File > Import > Transition List or direct past works without any intervening UI.

However, this is not necessarily teaching the students enough to make them successful on their own. It is, therefore, highly desirable that File > Import > Transition List or direct paste of what appears to be a small molecule transition list shows a column picker similar to what we now have for peptides. This can even allow for a transition list without column headers. The column picker can then also offer the ability to switch back and forth between Peptides and Small Molecules, like Edit > Insert > Transition List.

By far the best indicator of a proteomics transition list is a column with what can be interpreted as an amino acid sequence accompanied by a numeric column that has the matching precursor m/z for the peptide sequence. Strangely, however, the current logic first looks for column headers we feel are particular to small molecules and divert to small molecule handling if we see them regardless of what other columns are present. This logic could be improved, especially when faced with columnar data lacking a header row.

This is the most important area to continue working on the transition list column picking UI.