How to use the pyteomics.mass function in pyteomics

if annotation is not None:
            self._annotation = np.asarray(annotation).reshape(-1)
            if len(self.mz) != len(self.annotation):
                raise ValueError('The mass-to-charge and annotation arrays '
                                 'should have equal length')
            else:
                self._annotation = self.annotation[order]
        else:
            self._annotation = None

        self.retention_time = retention_time
        if peptide is not None:
            self.peptide = peptide.upper()
            for aa in self.peptide:
                if aa not in mass.std_aa_mass:
                    raise ValueError(f'Unknown amino acid: {aa}')
        else:
            self.peptide = None
        if peptide is not None and modifications is not None:
            for mod_pos in modifications.keys():
                if mod_pos not in ('N-term', 'C-term'):
                    if not isinstance(mod_pos, int):
                        raise ValueError(f'Unknown modification position: '
                                         f'{mod_pos}')
                    elif mod_pos < 0 or mod_pos > len(peptide):
                        raise ValueError(f'Modification position exceeds '
                                         f'peptide bounds: {mod_pos}')
        else:
            modifications = None
        self.modifications = modifications
        self.is_decoy = is_decoy