Mass Spec Results - mistaken as another isoform? - (Feb/14/2013 )
The protein I'm working with has a few isoforms sharing high similarity, and all of which showed up in the mass spec results. Upon analyzing the peptides from the other isoforms, they seem be to very similar to the isoform of interest.
EVPVVHTETK - peptide from the mass spec result (from a related isoform)
EVP I VQTETK - peptide from the isoform under study
Could the identification process 'mistakenly' assigned to a different isoform? If so, how about this? How many amino acid differences would consider as real?
LTSTDTIPK - peptide from the mass spec result (from a related isoform)
LVSPEQPPK - peptide from the isoform under study
According to my experience in mass spectrometry it is possible that it has taken another isoform by mistake. But I may be wrong also. Is this de-novo sequencing or you used some server to match the sequence to database? Because if we match with the database then chances of error are more. Also in isoforms where one amino acid can also make a difference, I have seen papers where people use multiple enzymes to digest protein and get the same sequence to confirm the results.