Clarification - C-terminal modifications

[Arthfael]

This is more of a theoretical question than a practical one: I have never worked with C-terminal PTMs before. But I find the explanations of the syntax for specifying where they apply in MSFragger slightly ambiguous:

Variable Modifications. Values: • A-Z amino acid codes • * is used to represent any amino acid • ^ is used to represent a terminus • [ is a modifier for protein N-terminal • ] is a modifier for protein C-terminal • n is a modifier for peptide N-terminal • c is a modifier for peptide C-terminal Syntax Examples: • 15.9949 M 3(for oxidation on methionine) • 79.66331 STY 1(for phosphorylation) • -17.0265 nQnC 1(for pyro-GIu or loss of ammonia at peptide N-terminal) Example (M oxidation and N-terminal acetylation): • variable mod 01 15.9949 M 3 • variable_mod 02 42.0106 [^ 1

So, if I want to have a C-terminal lysine, I guess I should write cK, correct? Or is it Kc? Similarly, for a protein C-terminus, I think it should be ^], not ]^, correct? I would also indicate to clarify - though it is obvious from the examples, e.g. for pyro-Glu which would technically be a "terminus" - that ^ is only necessary for protein termini.

[fcyu]

So, if I want to have a C-terminal lysine, I guess I should write cK, correct? Or is it Kc?

cK

Similarly, for a protein C-terminus, I think it should be ^], not ]^, correct?

]^

I would also indicate to clarify - though it is obvious from the examples, e.g. for pyro-Glu which would technically be a "terminus" - that ^ is only necessary for protein termini.

Not sure if I follow this one, but the pyro-Glu is at the peptide N-termini.

Best,

Fengchao

[Arthfael]

Thanks, the clarification was very much helpful ^^ I am still confused about ^, it feels unnecessary: since we already have unique marks for each type of terminus with c, n, [ and ], and also a special character ** for "any amino acid allowed", does ^* actually convey any information? Does it explicitly mean the actual -NH2 or -COOH at the respective terminus?

Kind regards,

Armel

On Tue, Sep 24, 2024 at 3:46 PM Fengchao @.***> wrote:

So, if I want to have a C-terminal lysine, I guess I should write cK, correct? Or is it Kc?

cK

Similarly, for a protein C-terminus, I think it should be ^], not ]^, correct?

]^

I would also indicate to clarify - though it is obvious from the examples, e.g. for pyro-Glu which would technically be a "terminus" - that ^ is only necessary for protein termini.

Not sure if I follow this one, but the pyro-Glu is at the peptide N-termini.

Best,

Fengchao

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[fcyu]

^ indicate the terminus not an amino acid.

Does it explicitly mean the actual -NH2 or -COOH at the respective terminus?

Correct.

Best,

Fengchao