In public database, 3D-conformations of the chosen chemicals were generated by omega after the removal of molecules with a hypervalent metal complex due to the assignment of charge under the Merck molecular force field (MMFF) [14, 37].
PepMatch module was used for evaluating the average abundance ratio of each sample peptide, allowing for automated detection of peptides and assignment of charge states.
This is because under low-energy conditions, the b-ion and y-ion fragments co-exist in a loose complex; the two members of this dimer compete for the proton, with assignment of charge being determined by the proton affinities of the two ions (Paizs and Suhai, 2004).
As a second step, atom-centered partial charges are computed according to the MMFF charge model [6], which requires assignment of formal charges.
Generally speaking, we avoid the assignment of formal charges, since this implies, in many cases, assumptions about the oxidation numbers of atoms or charge distribution within chemical moieties that are not always obvious, especially if we want to make such assumptions in a more or less automated way.
Many standard chemistry algorithms are included, for example, determination of the smallest set of smallest rings, bond order perception, addition of hydrogens, and assignment of Gasteiger charges.
The assignment of formal charges of Cu+, S- and S 2 2 − was actually based on the interpretation from X-Ray photoelectron spectroscopy (XPS) [45].
Particularly important was the assignment of positive charges in the connecting loops between the transmembrane helices to mimic the mutation experiments of Seppälä et al. (2010).
The docking procedure involved the preparation of the ligand and macromolecule, the assignment of Gasteiger charges, and the identification of the torsional root and the two rotatable bonds of the ligand.
Because deconvolution entails the assignment of a charge state and the recalculation of the m/ z's as if the charge were +1 (decharging), the combinatorial explosion problem mentioned above is automatically eliminated.
The presence of ions of the next or preceding oligomer can also help confirm the assignment of the charge state.
