Site specific variable mod search
Closed this issue · 5 comments
- Describe the feature:
I haven't found a direct way to do this, but am trying to set certain amino acids to only be searchable with variable mods. For instance looking at methylation on say 3 lysines for one protein and 1 specific lysine on another protein.
The closest I've been able to come is using U/O/J in my fasta and setting those as variable mods with the corresponding mass shifts. The problem is I have a larger search space than those three amino acids (closer to 10 mods, but only occuring on less than 20k potential sites).
I think in my idealized request we could denote lowercase amino acids in a fasta as custom masses to set variable mods to. I understand X can be denoted as custom mod, but as far as I know this is the only letter that allows this.
The closest I've been able to come is using U/O/J in my fasta and setting those as variable mods with the corresponding mass shifts. The problem is I have a larger search space than those three amino acids (closer to 10 mods, but only occuring on less than 20k potential sites).
If you count U and O, you actually have 6: BJXZUO. If 6 is not enough, I am sorry that there is not much we can do for now.
Best,
Fengchao
I think 6 would cover most of the search space, but my understanding is that B and Z are somewhat ambiguous in the mass to begin with. Is there a way to set those as more defined? I thought B is Asp or Asn so it can already be 115 or 114. I guess I don't understand how I can set this as a variable mod to be either methyllysine or acetyllysine when it has two masses to start.
Please let me know if there is a non-standard amino acid page I am missing. I have only inferred this from other github posts.
In MSFragger, U and O have non-zero masses, 150.95363 and 237.14773 respectively (I think I let MSFragger print these info in the log). BJXZ have zero masses. So, you could set your own masses using the statis mod options.
Best,
Fengchao
Thank you Fengchao, I think understand now. I can set a fixed mod mass for BJXZ in the GUI for my base and then set the difference for each in the variable section. I appreciate the help!
Correct, and you could also borrow U and O if they are not in your original fasta file. Just remember that U and O have their own masses. You need to take the subtraction.
Best,
Fengchao