The standard mass spectrometric technique for the analysis of phosphopeptides on a linear ion trap mass spectrometer is to perform MS/MS followed by MS3 of the putative neutral loss peak observed by MS/MS. This is usually termed data-dependent neutral loss MS3 (DDN-LMS3). The strength of this approach is the sensitivity in full scan MSn of linear ion trap technology and the characteristically strong neutral loss peak, which flags the MS/ MS spectrum as potentially belonging to a phosphopeptide. This approach has been much applied to phospho-proteomic analyses typically involving up-front phosphopeptide enrichment, such as TiO2 chromatography. Indeed, a recent article from Mann and co-workers identified 6600 phosphorylation sites utilizing a hybrid linear ion trap Fourier transform mass spectrometer. However, there are also weaknesses, such as the fact that phosphotyrosine residues rarely produce a neutral loss from the precursor during MS/MS
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