In the neutral loss scan type, the two mass analyzers (Q1 and Q3) link together so that they are scanned at the same rate over mass ranges of the same width. However, the respective mass ranges are offset by a selected mass so that the product mass analyzer scans a selected number of mass units lower than the precursor mass analyzer.
As a result, the neutral loss scan type provides two stages of mass analysis. In the first stage, the precursor mass analyzer (Q1) separates ions that form in the ion source by their m/z values. These ions enter the collision cell.
In the second stage of analysis, ions in the collision cell fragment by metastable ion decomposition or by CID to produce product ions. The product mass analyzer then separates these product ions by their m/z value.
To detect an ion, between the time the ion leaves Q1 and enters Q3, it must lose a neutral moiety whose mass (the neutral loss mass) is equal to the difference in the mass ranges being scanned by the two mass analyzers. Therefore, a neutral loss mass spectrum is a spectrum that shows all the precursor ions that lose a neutral species of a selected mass.
You can also perform a neutral gain (or association) experiment in which the mass range scanned by Q3 is offset by a selected mass above the mass range scanned by Q1.
For a neutral loss (or neutral gain) mass spectrum, as for a precursor mass spectrum, Q1 (the precursor ion) provides data for the m/z axis, whereas Q3 (the product ion being monitored) provides data for the ion intensity axis.
You can use experiments that use the neutral loss scan type (neutral loss experiments) when surveying a large number of compounds for common functionality. You frequently lose neutral moieties from substituent functional groups (for example, CO2 from carboxylic acids, CO from aldehydes, HX from halides, and H2O from alcohols).
The following figure shows examples of compounds with a common fragment ion.