as differential modifications (Figure 4). Figure 4. TurboSEQUEST software can accommodate multiple amino acid modifications in a single search routine. The search provided an unambiguous identification of the peptide (Figure 5), and confirmed the position of a phosphorylated residue. Note that the assigned peptide sequence GVVTNGLDLSPADEK contains two possible sites eligible for this modification (highlighted in blue). TurboSEQUEST analysis of MS/MS data reveals the serine residue as the site of phosphorylation (Figure 6). Figure 5. Neurofilament protein identified in TurboSEQUEST search. The peptide (in red) is phosphorylated at its serine residue (highlighted in green).

Figure 6. Fragments in the MS/MS spectrum of a phosphorylated peptide assigned by TurboSEQUEST search. The highlighted peak (*) represents a doubly-charged fragment corresponding to a neutral loss of phosphate from the original peptide. Conclusions We present here a simple strategy for the analysis of phosphorylated peptides, which can be achieved on any Thermo Finnigan LCQ series mass spectrometer. The combination of data dependent analysis and advanced TurboSequest database searching identifies candidate phosphorylated peptides in the LC/MS/MS data set, confirms the protein identity and sequence of the peptide, and assigns the exact position of the phosphorylated amino acid residue. References: 1. Betts, J.C., Blackstock, W.P., Ward, M.A., an
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