refine, spectrum synthesis

# refine, spectrum synthesis ## Syntax The parameter can have the values yes or no. ## Notes No error message is generated when an uninterpretable value is entered for this parameter. If no value is set, the default value is no. ## Description When X! TANDEM scores a model peptide sequence with a spectrum, it can take into account the probablity that a particular bond will break preferentially, relative to other bonds. yes - When this value is found, bonds N-terminal to proline residues and bonds C-terminal to aspartic acid, glutamic acid, valine, leucine, isoleucine, glutamine and asparagine are favoured. This process effectively predicts a "synthetic" spectrum and rewards ions that agree with the predicted spectrum. no - When this value is found, all bonds are considered to be equivalent. see also: refine X! TANDEM API description project