- Most of the proteins will undergo the tryptic digest. This means that the peptide
fragments will have either L or R at the C terminal side. So, it is easier to determine
that first, hence we start from the Y ion C terminal fragmentation side.
- Remember that we are trying to work out the sequence of one of the peptides
from the entire protein so still the C terminal here will be L or R.
- The residue masses that are given to us are the b ions -1 because in the B ions in the
N terminal end, that singular fragment has residue mass that is +1.
- For the Y ions, we must add +19 to the residue mass.
- The peaks are Y ion and B ion fragmentation peaks so we are writing those
corresponding to each residue on the top and bottom. So an important thing to
remember is that the peak does not mean one residue, it is a combination of
residues , but if we start from the end of the N terminal then we can build on with
different info through making subtractions and double checking with the other Y
fragment that corresponds to it.
- Because we know about the K and R situation, let’s start with the Y ion first. So, the
residue mass + 19. For K it is: 128+19=147. For R it is: 156+19 = 175. On the spectra
we can see a peak for the k, so this is the Y 1 ion. To find the corresponding B
fragment of the Y Ion is – 1163.8-147= 1016.8 and there is a peak for this, 1017.5 –
so those match up.
- Next, we can try looking for the B ions because the residue masses are easiest to
change there as opposed to the Y ion method.
fragments will have either L or R at the C terminal side. So, it is easier to determine
that first, hence we start from the Y ion C terminal fragmentation side.
- Remember that we are trying to work out the sequence of one of the peptides
from the entire protein so still the C terminal here will be L or R.
- The residue masses that are given to us are the b ions -1 because in the B ions in the
N terminal end, that singular fragment has residue mass that is +1.
- For the Y ions, we must add +19 to the residue mass.
- The peaks are Y ion and B ion fragmentation peaks so we are writing those
corresponding to each residue on the top and bottom. So an important thing to
remember is that the peak does not mean one residue, it is a combination of
residues , but if we start from the end of the N terminal then we can build on with
different info through making subtractions and double checking with the other Y
fragment that corresponds to it.
- Because we know about the K and R situation, let’s start with the Y ion first. So, the
residue mass + 19. For K it is: 128+19=147. For R it is: 156+19 = 175. On the spectra
we can see a peak for the k, so this is the Y 1 ion. To find the corresponding B
fragment of the Y Ion is – 1163.8-147= 1016.8 and there is a peak for this, 1017.5 –
so those match up.
- Next, we can try looking for the B ions because the residue masses are easiest to
change there as opposed to the Y ion method.
