Issue 675: View > Proteins and View > Peptides menu items added and remove View > Targets

Assigned To:Guest
Opened:2019-08-21 by Brendan MacLean
Changed:2021-11-30 by Brendan MacLean
Resolved:2019-12-03 by Nick Shulman
Closed:2021-11-30 by Brendan MacLean
2019-08-21 Brendan MacLean
Title»View > Proteins and View > Peptides menu items added and remove View > Targets
Assigned ToGuest»Brendan MacLean
What is now View > Targets, I believe, was once View > Proteins.

In proteomics mode, it offers the options:
By Name
By Accession
By Preferred Name
By Gene

Everything in the list but "By Name" applies only to proteins. The term "Targets" is too general. In some sense, it seems applies more to the molecular level than the molecular-grouping / protein level, but it is also general enough to apply to even the precursor level (i.e. molecule + adduct).

When you switch to small molecule UI, this menu item remains but is reduced to containing just 1 option:
By Name

This is useless, a list of options with one option.

Instead we should change the top-level menu item back to Proteins and have it removed entirely in small molecule UI mode. That is, you can't control seeing proteins by Name/Accession/Preferred Name/Gene when you are not in proteomics mode.

This makes even more sense in the context of our recently being asked to add options for how peptides get shown. Currently, they can only be shown as the bare peptide sequence with modified amino acid residues highlighted (bold and underlined for structural or colored for isotope modifications), but we've been requested to add a way to show the modification datails in the Targets view, which will lead to a View > Peptides menu item with options like:
By Sequence
By Mass Modified Sequence
By Three Letter Modified Sequence
By Full Name Modified Sequence
By Unimod Ids Modified Sequence

I have decided to combine these two issues so that both will get implemented at the same time.

2019-10-08 Brendan MacLean
Assigned ToBrendan MacLean»Nick Shulman
I think this probably works fine and that View > Targets was a mistake. Though, maybe your View > Modifications is better than View > Peptides. The highlighting should stay on the amino acid and the modification text also, since the highlighting can be colored, bold, underlined.

2019-12-03 Nick Shulman
resolve as Fixed
Assigned ToNick Shulman»Brendan MacLean
Options to control the display of modifications were added on November 25.

There are sub menu items "View > Modifications": "Not Shown", "Mass Difference", "Three Letter Code" and "Full Name" and "Unimod ID".

2021-11-30 Brendan MacLean
Assigned ToBrendan MacLean»Guest