How Are Peptides Named in BPV Flex Software after in Silico Digestion?

For research use only. Not for use in diagnostic procedures.

Answer

After importing a protein sequence into BPV Flex software, the software will predict potential cleavage sites recognized by a designated protease and then display the predicted peptides, which are named following a specific naming convention. The general rule for naming peptides in BPV Flex software is: the first peptide resulting from a proteolytic cleavage is named T1 for sequences displayed from the N-terminus to the C-terminus; moving toward the C-terminus, the second proteolytic cleaved peptide is named T2, and so forth. If there is a missed cleavage, the resulting longer peptide is named for the theoretical peptide from either side of the missed cleavage.

For example, below if the selected peptide sequence is QVTLRESGPALVKPTQTLTLTCTFSGFSLSTAK, which is then digested in silico with trypsin with one one missed cleavage allowed, the following names would apply:

• QVTLR would be named T1
• ESGPALVKPTQTLTLTCTFSGFSLSTAK would be named T2
• If there is a missed cleavage, then QVTLRESGPALVKPTQTLTLTCTFSGFSLSTAK would be named T1-T2.