Paste of peptides with PTMs misses some peptides

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Paste of peptides with PTMs misses some peptides Nathan Manes  2019-04-11
 

A new bug seems to have popped up in v4.2.0.19072. If a text list of peptides with PTMs is copy-pasted into Skyline such as:
IADPEHDHTGFLTEYVATR[Label:13C(6)15N(4) (R)]
IADPEHDHTGFLTEY[Phospho (Y)]VATR[Label:13C(6)15N(4) (R)]
then only the first peptide is in the resulting list of peptide targets. If the second peptide is pasted again, it appears. Note that Edit ---> Insert ---> Peptides works correctly.

 
 
Nick Shulman responded:  2019-04-11
This seems to work correctly for me, but I might not understand your steps correctly.

Are you saying that you have that text on the clipboard, and then you press the paste button into an empty Skyline document and you only get one peptide?
I have attached a PowerPoint showing pictures of what I think your steps are.
-- Nick
 
Nathan Manes responded:  2019-04-11
It's even stranger than I thought. If you paste into a completely empty target list, everything works normally (I hadn't noticed that). If you start with a totally empty target list and manually enter a protein name and then paste, the bug happens.
 
Brendan MacLean responded:  2019-04-12
I see what you mean. If I paste those 2 lines onto the empty element (dotted box) in the Targets view, the paste goes as expected and a new peptide list is created with both of the peptide forms. Same is true if I paste with a sequence-backed protein element selected. A new peptide list gets created with both forms. But if I paste onto an existing list, then only the first form gets added to the list.

Looks like we must be doing some kind of ignoring based on the bare peptide sequence instead of the modified sequence, because when I use this list in the same way, I get only 2 new peptides, the first pasted of each sequence:

IADPEHDHTGFLTEYVATR[Label:13C(6)15N(4) (R)]
IADPEHDHTGFLTEY[Phospho (Y)]VATR[Label:13C(6)15N(4) (R)]
PESTIDER
PEST[Phospho (ST)]IDER
PES[Phospho (ST)]TIDER
PES[Phospho (ST)]T[Phospho (ST)]IDER

Thanks for the bug report. I am sure it won't take long to fix.

--Brendan