From an email thread 11/7/2022 with Nick, Phil Remes, Brendan, BrianP

Brendan,

It looks like "File > Import > Transition List" doesn't know how to deal with the "Special Ions" that might be listed on "Settings > Transition Settings > Filter".
Philip Remes has a huge transition list with many TMT and non-TMT transitions in it.
Is there any way that he could get all of those transitions into the document?

One thing that I thought would work would be first to have a document with all of the TMT transitions in it, and then use "File > Import > Transition List" to import a CSV file containing all of the non-TMT transitions in it, and then he would end up with peptides with the complete set of transitions that he wants. Unfortunately, doing that always results in a second peptide group being created, so that there is no peptide in the document which contains the complete set of transitions that it is supposed to.

Can you think of a way for Philip to get all of the transitions into the document?

I'm thinking we should just fix it so that MassListRowReader knows what to do when it sees a transition whose m/z matches a Special Ion.
-- Nick

Nick adds:

I wonder if we should combine fixing this bug with this other bug that's currently assigned to Rita:
Issue 352: Annotate reporter ions in Library Match graph

There are at least three different places in the product where we call "SequenceCalc.GetFragmentIonMasses".
Those places are:
TransitionGroup.GetTransitions: populating the list of transitions that could be added to a TransitionGroup
MassListRowReader.CalcTransitionExplanations: importing a transition list
SpectrumRanker constructor: Annotating ions in a library spectrum

In each of those places we've either already added or will have to add in the future code to deal with neutral losses, reporter ions, and crosslinked peptides.
I am pretty sure that each of those things should know about exactly the same types of ions, and any differences in the implementation in those areas will lead to bugs.

I imagine we should probably centralize that logic somewhere so that no one calls "GetFragmentIonMasses" directly.
-- Nick