refine, spectrum synthesis

Syntax

The parameter can have the values yes or no.

Notes

1. No error message is generated when an uninterpretable value is entered for this parameter.
2. 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.

1. 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.
2. no - When this value is found, all bonds are considered to be equivalent.