US Patent 7511267 Data-dependent accurate mass neutral loss analysis

A method is disclosed for data-dependent neutral loss analysis of biomolecules and other materials in a hybrid mass spectrometer. Candidate product ions are selected by identifying peaks in a MS/MS spectrum acquired in a first mass analyzer that exhibit a specified nominal neutral loss value, which may be representative of the mass of a peptide modification, such as phosphate. High mass accuracy MS and MS/MS spectra acquired at a second mass analyzer, such as an FTICR or Orbitrap, are processed to determine if the mass difference between a candidate product ion and its corresponding precursor matches an accurate neutral loss value. In one embodiment, MS3 analysis is performed only on the candidate product ions that satisfy the accurate mass neutral loss value test.