What is the advantage of neutral loss detection in phosphoproteomics?
The localization of phosphorylation sites in peptide sequences is a challenging problem in large-scale phosphoproteomics analysis. The intense neutral loss peaks and the coexistence of multiple serine/threonine and/or tyrosine residues are limiting factors for objectively scoring site patterns across thousands of peptides.
CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group  allowing detection and sequencing of phosphopeptides.