protein, quick pyrolidone

Syntax

The parameter can have the values yes or no.

Notes

1. Default value = yes.
2. Introduced in version 2010.01.01.1.

Description

Peptides that have N-terminal glutamine (Q) residues in solution will spontaneous form the cyclic pyrolidone derivative by the loss of NH₃ (-17 Da). A similar solution phase reaction can occur with peptides with N-terminal glutamic acid residues through the loss of H₂O (-18 Da) or for N-terminal cysteine residues that have been chemically blocked using iodoacetimide, through the loss of NH₃ (-17 Da). When this parameter is yes, these derivatives are checked, as well as the underivatized forms of the residues. Using this parameter is a much more efficient calculation than using the potential modifications "-17@[" or "-18@[".

This behavior has always been the default for X! Tandem: this parameter allows users to control this behavior. It is HIGHLY recommended that this parameter be set to yes unless there is a good reason not to check for this very common modification.