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Elsevier, Journal of Proteomics, (103), p. 1-14

DOI: 10.1016/j.jprot.2014.03.010

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Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation☆

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

•We report and benchmark a data analysis pipeline for phosphoproteomic data analysis.•Combined use of Mascot Percolator and turbo-SLoMo to compare fragmentation methods•CID and ETD fragmentation for phosphorylation site identification•Demonstrate the utility of data-dependent neutral loss triggered ETD fragmentation•High confidence of phosphoproteomic analysis using ETD/CID spectral pairs