spectrum, minimum fragment mz

Syntax

This value is a positive floating point number, Mfmin.

Notes

  1. If no value is specified or it is uninterpretable, the default value is Mfmin = 200
  2. No error message is generated by inappropriate values.

Description

The fragment ion mass spectra produced by peptides contain peaks that are sequence-specific and those that are caused by individual amino acid residues. The peaks caused by these individual amino acid residues tend to be relatively small (m/z < 200) and they do not affect the outcome of a search. However, these peaks can be very intense, sometimes dwarfing the sequence-specific peaks used by TANDEM to discover appropriate model peptide sequences. The value of Mfmin is used to remove these intense (but not very useful) peaks, prior to normalization. Any peak that does not meet the condition:

m/z > Mfmin

is rejected.

see also: spectrum, dynamic range | spectrum, minimum parent m+h
spectrum, minimum peaks | spectrum, use noise suppression

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