spectrum, fragment mass type

Syntax

The value for this parameter is an ASCII string, with two possible values: average or monoisotopic

Notes

1. If this parameter is not present or set to a unexpected value, the default value monoisotopic will be used.
2. No error message is generated when a bad value is used for this parameter.

Description

Naturally occuring organic molecules do not have a single value corresponding to the "mass" of the molecule. Because organic molecules contain carbon, any collection of molecules will have some probability of containing one or more ¹³C atoms. In mass spectrometry, it is common to refer to the weighted average of all possible ¹³C-containing molecular masses as the "chemical" or "average" mass of the molecule. When this parameter is set to average, this weighted average is used to calculate the masses of the fragment ions in a tandem mass spectrum.

Most modern mass spectrometers have sufficient mass resolution so that the mass of each of the individual ¹³C-containing species can be measured separately. The lowest mass of these peaks will contain only ¹²C atoms. This lowest mass peak in the isotopic distribution measured is commonly refered to as the "monoisotopic" mass for the molecule (also refered to as the A0 peak). When this parameter is set to monoisotopic, this peak is used to define the mass of the fragment ions.