spectrum, fragment mass error

Syntax

The value is a floating point number (T_f > 0.0), represented as a character string.

Notes

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

Description

The measurement of fragment ion mass values may result in either monoisotopic masses, or chemical average masses. When spectrum, fragment mass type is set to average, this value is used, otherwise the value supplied for spectrum, fragment monoisotopic mass error is used.

The fragment ion mass error is the most important single parameter in finding a good peptide model for a tandem mass spectrum. For example, if a fragment ion has a measured mass of m₁ and a mass p₁ is predicted from a peptide sequence, then the difference between the two masses (d₁) is given by the following:

d₁ = | m₁ - p₁ |

If d₁ < T_f, then the fragment is considered as found. Otherwise, the fragment is ignored, without penalty. Peptide modeling for identification depends strongly on counting the number of predicted fragments that are found in a spectrum, so setting this value correctly will determine the success or failure of an identficiation. It is worthwhile to experiment with this value when using a new instrument, to determine the best settings for identifying a known set of peptides.