spectrum, parent monoisotopic mass error minus

Syntax

The value is a positive floating point number (T_-p), represented as a character string.

Notes

1. Interpretation of this value depends on the value set for spectrum, parent monoisotopic mass error units.
2. TANDEM inserts a default value for this parameter if it doesn't exist or is set to 0.0.

Description

TANDEM uses this value as part of the calculation to determine if a particular peptide sequence is to be considered as a possible model for a spectrum. The calculated mass of the peptide is compared with the value using the following expression, where m_p and p_p are the measured mass from the spectrum and the calculated mass from the candidate peptide, respectively:

d = m_p - p_p

If the conditions d < 0 and T_-p > -d are met, then the peptide is a candidate sequence.

This condition (as well as the "plus" condition) are used to limit the extent of the more elaborate fragment by fragment calculations that are performed to truly match a peptide with a spectrum. From a mathematical point of view, if these conditions are not met, the peptide sequence is assigned a score of -∞ and discarded.

Most protein identification tools use a single parameter for this type of matching, requiring a symmetric condition T_p < |d|. TANDEM allows the user to set assymetric values for the parent ion mass error, to compensate for the assymetric systematic mass errors generated by some types of mass spectrometers, particularly the currently popular ion trap instruments.