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Detection and Identification of Phosphorylation Sites in Proteins Using ,,, LC/MS/MS with Neutral Fragment Loss Mapping

veyor LC and LCQ Deca XP. The data acquisition process included a full MS scan followed by a full MS/MS scan of the most intense ion selected from the preceding MS spectrum.

Phosphorylated peptides exhibit the loss of a phosphate group during fragmentation in an ion trap (Figure 1). A prominent ion corresponding to a dephosphorylated peptide is usually observed in the MS/MS spectrum. The neutral loss profile display is used to locate a specific neutral loss in the acquired data (Figure 2). In this example, the loss of 49 amu corresponds to the difference between the precursor ion mass of a doublycharged phosphorylated peptide and its dephos-phorylated variant, observed in its MS/MS spectrum. This conveniently highlights any possible phosphopeptide candidates within a given data set (Figure 3). Figure 2. Setting up a neutral loss profile.

Figure 3. A neutral loss profile detecting a neutral loss of 49 amu (assuming doubly charged species) identified possible phosphorylated candidate peptides from Figure 1. (A) Base peak chromatogram; (B) Neutral loss profile. The peptide is then identified by a TurboSEQUEST database search that also confirms the exact location of the phosphorylation residue within the peptide sequence. The TurboSEQUEST search engine, within the BioWorks 3.0 protein identification software suite, can accommodate multiple amino acid modifications in a single search routine. In this case, an alkylation was considered for all cysteine residues in the sequence (a static modification), while oxidation of methionine and phosphorylation of serine and threonine were treated
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