The original article is from KG Kuznetsova et al., and can be found here. (Side note: Man, there has been some cool original research coming out of Moscow lately! Keep it coming!)
Wait. What is Isothreonine again? Well, its also called homoserine and we sometimes see it in proteomics data, but it generally isn't a good thing.
Check out this quick image I borrowed from Alexey Chernobrovkin et al., from this paper a couple years ago:
In this illustration, the protein is yanked out and digested and...crud...overheating the protein with iodoacetamide converts some of the methionines to isothreonines. Gross. Then, cause you don't have IsoThreonine in your FASTA, you end up finding a peptide with regular old Threonine in it.
1) De novo sequencing (nuts) -- you totally got a peptide wrong
2) Proteogenomics -- cause your huge database has lots and lots of possibilities in it. And...well...the chances that you'll have a peptide sequence in your database with a xxxTxxxK (from a peptide that really started out as xxxMxxxK...but isn't there anymore is higher than when you are using a smaller, manually curated FASTA and your odds of making that mismatch is made higher just algebraically.
All is not lost, researchers who are banking hard on proteogenomics/metagenomics being the future!
Cause the original paper I found at the top did a focused study with synthetic peptides and found 1) the Isothreonine peptides elute differently AND there is a change in the HCD fragmentation patterns (actually the second paper I mention reports that as well), but they suggest that it would be reasonably easy to integrate this shift in fragmentation patterns into most proteogenomic pipelines!
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