FIG.4.

Identification of a phosphopeptide from a novel protein of unknown function (gene model C_50124) by neutral-loss-triggered nano-LC-ESI-MS³. (A) Full MS scan in the m/z range of 500 to 600 detects the prominent peptide ion 546.7. (B) The MS² fragmentation spectrum of peptide ion 546.7 reveals the neutral loss (fragment ion 497.4) but no fragment information sufficient for peptide identification. (C) Identification of the peptide KAAGFFG(MeDha)GR by neutral-loss-triggered MS³ of peptide ion 479.4. “MeDha” indicates the site of the neutral loss of phosphoric acid from the phosphothreonine. Only prominent y- and b-fragment ions have been labeled.