refine

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

X! TANDEM uses a process called "refinement" to improve the speed and accuracy of peptide modelling. When the parameter value is yes, then the refinement process is used, otherwise X! TANDEM functions like other sequence modelling engines.

The algorithm used by Tandem is an example of possible algorithms that belong to this class of methods for obtaining similar results. Variations of the scheme may be necessary to adequately capture all of the details of specific experimental protocols. The steps in a simple refinement-based identification/modeling process are as follows:

1. Match a set of tandem mass spectra containing a large set of spectra against a list of proteins, with a small value for the number of missed cleavages (e.g., 0 or 1) and a limited selection of potential modifications and create a set of protein sequences that are most likely to contain valid matches to the spectra (e.g., all proteins containing peptides with an expectation value < 0.1);
2. Match the tandem spectra against the new, smaller list of protein sequences, using a large value for the number of missed cleavages and a large selection of potential modifications; and
3. If desired, perform the same matching procedure as step 2, using nonspecific hydrolysis.