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The chemical and physical diversity of post-translational modifications (PTMs) of proteins presents a challenge in determining their structure and function. Liquid chromatography–mass spectrometry (LC-MS) is currently the method of choice for the analysis of protein modifications, but a proper workflow has to be developed and applied to each modification studied. This chapter presents major challenges in the identification of PTMs by LC-MS and discusses a protocol for large-scale enrichment and LC-MS analysis of protein phosphorylation.

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