Jake Jaffe highlighted a case where the following two reference lines and their attendant spectra get merged, and essentially only the first spectrum is represented.

full_spectral_library.ms2    6    2    T[56.0262]K[42.0470]QTAR[10.0083]
full_spectral_library.ms2    7    2    T[56.0262]K[42.0106]QTAR[10.0083]

The relevant modifications are propionyl (56.0262), trimethyl (42.0470), acetyl (42.0106), and SILAC R10 (10.0083) in this case.

Unfortunately, quite a lot inside Skyline currently assumes that amino acid and a single decimal place are sufficient to differentiate all known modifications (obviously not for this case).

Supporting the highlighted case will mean rethinking this assumption and fixing both library building and Skyline internal modification annotation to get this working.

I am going to assign this to Kaipo. I hope we can fix this with the new work on peptide modified sequence keys that Nick has taken over. Though, this may still require new work from Kaipo on the BlibBuild side.

Maybe something for Nick to think about as he has this hot potato now.

This got fixed in Skyline 4.1.