spectrum, minimum peaks

Syntax

The value is a non-zero, positive integer, Nmin.

Notes

  1. If this value is absent or uninterpretable, a default value of 5 is used.
  2. If a floating point number is used, rather than an integer, normal C truncation is used for conversion to an integer value.
  3. No error messages are generated for out-of-range values.

Description

The MS/MS spectra used in peptide sequence searches are composed of a limited number of mass-to-charge ratio:intensity pairs. Many common types of mass spectrometer data systems will generate a mass spectrum during a chromatographic run, even if the parent ion does not fragment. The value of this parameter is used to screen out spectra that contain too few fragment ions to be usefully interpreted.

If the total number of mass-to-charge ratio:intensity pairs is a particular spectrum is N, then the condition that a spectrum is considered to have too few ions to be considered would be:

N < Nmin

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

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