Pseudo-neutral-loss scan for selective detection of phosphopeptides and N-glycopeptides using liquid chromatography coupled with a hybrid linear ion-trap/orbitrap mass spectrometer

We describe a novel method, termed pseudo-neutral-loss scan'' MS, for selectively probing phosphopeptides and glycopeptides on a LTQ-Orbitrap mass spectrometer. The instrument has been programmed such that an in-source CID energy is applied to all species that eluted from LC column and were subsequently ionised in the electrospray ion source. Ion pairs that differ in the mass of a neutral loss of phosphoric acid or monosaccharide residues are automatically selected for CID MS/MS and further for multi-stage-activation MS3. Our method should prove useful for a highly selective and sensitive approach to identify phosphopeptides and glycopeptides from purified protein digestion without any further enrichment, and could potentially be of use in more complex mixture.