What is neutral loss?
This expression refers to the loss of a neutral fragment from a molecule. Generally, neutral molecules are acetic acid, phosphoric acid, or other low molecular weight molecules. A neutral molecule is formed when an acetyl or phosphate group takes a hydrogen from a specific position in the complete molecule. This process occurs in the collision cell (although it may also occur in the nozzle separator region, where the spray enters the ion source). The neutral loss of 98 (H3PO4) can be used to detect phosphorylated peptides because the energy required for neutral loss fragments is lower than that required to break the peptide backbone.
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