spectrum, fragment mass error
The value is a floating point number (Tf > 0.0), represented as a character string.
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 < Tf, 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.
see also: spectrum, fragment mass error units | spectrum, fragment mass type |
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