spectrum, total peaks

Syntax

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

Notes

  1. If this value is absent or uninterpretable, a default value of 50 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 mass spectrometer data systems will record large numbers of peaks in a particular spectrum, even though most of these peaks are simply noise.

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 many ions if the following statement is true:

N > Nmax

If this condition is met, then the Nmax most intense peaks are used by TANDEM to find the best protein model for the spectrum.

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

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