SP19A Phosphoprotein profiling by negative mode precursor ion scanning |
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Authors: | W Old J B Shabb C Yen S Houel B Eichelberger C Croy K A Resing N G Ahn |
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Institution: | 1.University of Colorado at Boulder, Boulder, CO, United States.;2.University of North Dakota, Grand Forks, ND, United States. |
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Abstract: | An important goal in cancer research is to monitor phosphoprotein changes in order to identify downstream targets of dysregulated signaling pathways. We used a precursor ion scanning approach described by Carr et al,1 which identifies phosphopeptides in negative ion mode by their loss of a −79-Da signature ion (PO3−). We first compared three methods for phosphopeptide detection in the protein kinase, Mps1. Using a 4000 QTrap mass spectrometer, standard analysis by LC/MS/MS in positive mode identified 27 phosphopeptides containing 22 phosphosites. Precursor ion scanning in negative mode using the same instrument identified 47 phosphopeptides containing 34 phosphosites, with detection sensitivity ~10 fmol. Using a LTQ-Orbitrap mass spectrometer, MS3 on peptide ions that underwent neutral loss of H3PO4 during MS/MS identified 30 phosphopeptides and 28 phosphosites. Thus, precursor ion scanning showed the highest performance in identifying phosphopeptides in simple mixtures.Next, we examined human melanoma cells treated with and without U0126, a drug that inhibits the constitutively activated B-Raf/MAPK pathway. Cytosolic proteins were resolved by SAX-FPLC, and proteins in each fraction were proteolyzed. Peptides in each fraction were separated by nanoflow RP-HPLC and phosphopeptides monitored by precursor ion scanning, triggering MS/MS upon detection of the −79-Da signature ion. In parallel, peptides were analyzed by positive mode LC/MS/MS in order to monitor protein abundance changes by spectral counting. In-house algorithms utilizing OpenMS modules were developed to detect phosphopeptide peaks, match them to MS/MS spectra, group peaks over consecutive fractions, and quantify and sum intensities. More than 20,000 peaks could be detected over all SAX fractions, representing ~5000 grouped phosphopeptide candidates. About 350 phosphopeptides were manually validated, of which ~10% were responsive to drug treatment. Thus, targets of dysregulated B-Raf/MAPK signaling in melanoma can be identified using precursor ion scanning and detection of phosphopeptides in complex samples. |
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