[GeorgWa]

Add msfragger mass mappings and SMILES for heavy dimethyl modifications:

• Dimethyl:2H(4) (medium label)
• Dimethyl:2H(6)13C(2) (heavy label)
• Dimethyl:2H(4)13C(2)
• Dimethyl:2H(6)

[Copilot]

Pull request overview

This PR adds support for dimethyl isotope label modifications in MSFragger by adding mass mappings and SMILES structures for various heavy dimethyl variants.

• Adds MSFragger mass mappings for dimethyl isotope modifications (light and heavy labels)
• Updates SMILES structures for dimethyl isotope modifications to represent the complete molecular structure
• Ensures consistency across K (lysine) and N-terminal modification sites

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.

File	Description
alphabase/constants/const_files/psm_reader.yaml	Adds MSFragger mass mappings for dimethyl isotope modifications on K and N-term sites
alphabase/constants/const_files/modification.tsv	Updates SMILES structures for dimethyl isotope label modifications

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[Copilot]

The SMILES structures use [Ts] (tosyl group) as a placeholder, which is unconventional for representing N-terminal dimethylation. Standard SMILES notation for dimethylation should represent the two methyl groups attached to the nitrogen without tosyl groups. Consider using a more appropriate SMILES representation for the actual chemical structure.

Suggested change

	Dimethyl:2H(6)13C(2)@Any_N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 [13C]([2H])([2H])([2H])[Ts][13C]([2H])([2H])([2H]) 0.0
	Dimethyl:2H(6)13C(2)@Any_N-term 36.07567 36.0754 H(-2)2H(6)13C(2) 0.0 Isotopic label 330 [N]([13C]([2H])([2H])[2H])([13C]([2H])([2H])[2H]) 0.0

[Copilot]

The SMILES structure uses [Fl] (likely fluorine) placeholders in the notation N([Fl])([Fl]), which is chemically invalid as nitrogen cannot be bonded to two separate fluorine atoms in this context. The complete lysine structure should be represented more accurately or the SMILES should focus only on the modification group.

[Copilot]

Inconsistent hydrogen representation in SMILES across different isotope variants. Some use ([2H])([2H])([1H]) explicitly showing hydrogen atoms while others use ([2H])([2H]) without explicit hydrogen. For clarity and consistency, consider using a uniform notation pattern across all dimethyl isotope modifications.

Suggested change

	Dimethyl:2H(4)@Protein_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])[Ts]C([2H])([2H]) 0.0
	Dimethyl:2H(4)@Any_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])[Ts]C([2H])([2H]) 0.0
	Dimethyl:2H(4)@K 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])N(C([2H])([2H]))CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts] 0.0
	Dimethyl:2H(4)@Protein_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])([1H])[Ts]C([2H])([2H])([1H]) 0.0
	Dimethyl:2H(4)@Any_N-term 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])([1H])[Ts]C([2H])([2H])([1H]) 0.0
	Dimethyl:2H(4)@K 32.056407 32.0778 2H(4)C(2) 0.0 Isotopic label 199 C([2H])([2H])([1H])N(C([2H])([2H])([1H]))CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts] 0.0

[Copilot]

Inconsistent hydrogen representation in SMILES across different isotope variants. Some use ([2H])([2H])([1H]) explicitly showing hydrogen atoms while others use ([2H])([2H]) without explicit hydrogen. For clarity and consistency, consider using a uniform notation pattern across all dimethyl isotope modifications.

[Copilot]

Inconsistent hydrogen representation in SMILES across different isotope variants. Some use ([2H])([2H])([1H]) explicitly showing hydrogen atoms while others use ([2H])([2H]) without explicit hydrogen. For clarity and consistency, consider using a uniform notation pattern across all dimethyl isotope modifications.

[lucas-diedrich]

LGTM

Would it make sense distinguish alphabase.smiles.smiles.MOD_N_TERM_PLACEHOLDER_ATOM=Ts and alphabase.smiles.smiles.C_TERM_PLACEHOLDER_ATOM=Ts semantically?