|Title||»||Transition list reader should identify special ions by m/z the same way it does calculated peptide fragment ions|
|Assigned To||»||Brian Pratt|
From an email thread 11/7/2022 with Nick, Phil Remes, Brendan, BrianP
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.