Menu
▾
▴
#262 Fix how terminal mods are represented within peptide sequences
When printing a peptide with modifications in brackets, terminal modifications should be represented as they are in Comet, namely, using "n" for N-terminal modification and "c" for C-terminal modification. I don't know whether peptide and protein-level terminal mods are discriminated -- I will ask Jimmy this.
Here is what Jimmy said:
"There's no special designation that a terminal modification is a protein terminal mod vs. a peptide terminal mod. So the modified peptide string might look like this:
R.n[17]DHLFFADLKPEKIMGENYLc[33].Y 1_V_15.994900_n, 19_V_15.994900_c
I've gone back and forth between reporting the mass difference vs. the modified mass in the peptide string. For the Crux compiled version, the masses in the peptide string look like the above where the mass value in the bracket is the modified mass value."
Kaipo, is this consistent with what Tide does?
I'm not quite understanding where the 17 and 33 come from, if the mass of the modification is 15.9949?
In tide, it will look like: D[15.99]HLFFADLKPEKIMGENYL[15.99]. The masses are just appearing as though they are modifications on the first/last AA in the sequence, since we are not showing flanking AA in the sequence column (though with the new modifications column we can still know they are terminal modifications).
I asked Jimmy about the 17 and 33.
But I think the idea is that a terminal amino acid can have two different
mods on it -- terminal and non-terminal. We need to be able to represent
that in the output. So Jimmy could do something like n[3]H[4]LFFADLK for an
n-term mod of 3 and an additional mod of 4 on the initial residue. Can you
make it so that Tide does something similar?
Bill
On Wed, Jun 22, 2016 at 3:14 PM, Kaipo kaipot@users.sf.net wrote:
Related
Issues: #262
Here is what Jimmy said about the 17 and 33:
That's the "modified mass" value I mentioned with respect to "mass difference" and "modified mass".
It would be the equivalent of representing oxidized methionine M[147] instead of M[16] where 147 = 131+16.
N-terminal group mass is H or 1.0078 so 1+16 = 17 hence n[17].
C-terminal group mass is OH or 17.0 and 17.0+16 = 33 hence c[33].
A couple of people who were using the Comet text output complained when I switched from using the mass difference (M[16]) to the modified mass (M[147]) so I switched back to showing mass differences. We can do this for the Comet-Crux text output too if you prefer. In that case, the peptide would look like something like:
Sure - I guess we should only output the n/c if there is a terminal modification? Also, I wonder if the indices in the modifications column should be 0 and <length of="" sequence+1=""> for the terminal modifications (rather than 1 and <length of="" sequence="">)?</length></length>
On Wed, Jun 22, 2016 at 3:54 PM, Kaipo kaipot@users.sf.net wrote:
Right.
Bill