We demonstrate a strategy employing collision-induced dissociation for phosphopeptide discovery, followed by targeted electron capture dissociation (ECD) for site localization. The high mass accuracy and low background noise of the ECD mass spectra allow facile sequencing of coeluting isobaric phosphopeptides, with up to two isobaric phosphopeptides sequenced from a single mass spectrum. In contrast to the previously described neutral loss dependent ECD method, targeted ECD allows analysis of both phosphotyrosine peptides and lower abundance phosphopeptides. The approach was applied to phosphorylation analysis of human Sprouty2, a regulator of receptor tyrosine kinase signaling. Fifteen sites of phosphorylation were identified, 11 of which are novel.Phosphorylation is a widespread and biologically significant protein post-translational modification.1 Phosphopeptide discovery is becoming more routine, thanks largely to improved enrichment methods and higher speed mass spectrometers.2,3 However site localization from collision-induced dissociation (CID) mass spectra remains a challenge, particularly for larger phosphopeptides with multiple potential phosphorylation sites.4 Low-energy CID fragmentation of phosphopeptides frequently results in losses of phosphoric acid, in addition to the typical CID losses of water and ammonia, thus complicating manual analysis.5-7 Bioinformatic approaches to automation of site localization have recently been published. 8,9 While automation streamlines the localization process, many CID spectra still give ambiguous results, e.g., 39 and 33% of sites in two recent large-scale studies where confidence of site localization was quantified. 8,10 Site-directed mutagenesis is commonly used in order to decipher the functional significance of phosphorylation for a given protein.11 If site-directed mutagenesis is to be carried out, obtaining accurate localization data for as many sites of phosphorylation as possible is particularly important, in order to avoid lengthy and costly analysis of inappropriate residues.Alternative mass spectrometric methods for site localization include MS 3 of the H 3 PO 4 neutral loss product ion, negative mode CID, and non-CID radical-driven fragmentation. Neutral loss dependent MS 3 spectra have been used to increase confidence in phosphopeptide identifications; 9,12-14 however, their contribution to site localization has not been rigorously described. Jiang et al. used information from paired MS 2 and MS 3 spectra to localize the site of phosphorylation, but neither the relative contributions to localization from the different scan types nor the confidence of site localization was reported.12 Beausoleil et al. found that MS 3 spectra provided little additional localization information, an observation that was ascribed to reduced ion statistics in MS 3 spectra. 8 An additional caveat is that the neutral loss of water from unmodified residues results in a fragment of the same mass as loss of H 3 PO 4 from a phosphorylated residue.
7,15The use of negative ion...