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Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

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    Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons
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    † Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
    ‡ Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
    § Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
    *E-mail: [email protected]
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2017, 16, 2, 728–737
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    https://doi.org/10.1021/acs.jproteome.6b00753
    Published November 28, 2016
    Copyright © 2016 American Chemical Society
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    Abstract

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    Because of the low stoichiometry of protein phosphorylation, targeted enrichment prior to LC–MS/MS analysis is still essential. The trend in phosphoproteome analysis is shifting toward an increasing number of biological replicates per experiment, ideally starting from very low sample amounts, placing new demands on enrichment protocols to make them less labor-intensive, more sensitive, and less prone to variability. Here we assessed an automated enrichment protocol using Fe(III)-IMAC cartridges on an AssayMAP Bravo platform to meet these demands. The automated Fe(III)-IMAC-based enrichment workflow proved to be more effective when compared to a TiO2-based enrichment using the same platform and a manual Ti(IV)-IMAC-based enrichment workflow. As initial samples, a dilution series of both human HeLa cell and primary rat hippocampal neuron lysates was used, going down to 0.1 μg of peptide starting material. The optimized workflow proved to be efficient, sensitive, and reproducible, identifying, localizing, and quantifying thousands of phosphosites from just micrograms of starting material. To further test the automated workflow in genuine biological applications, we monitored EGF-induced signaling in hippocampal neurons, starting with only 200 000 primary cells, resulting in ∼50 μg of protein material. This revealed a comprehensive phosphoproteome, showing regulation of multiple members of the MAPK pathway and reduced phosphorylation status of two glutamate receptors involved in synaptic plasticity.

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    • Percentage of S, T, and Y phosphorylation and phosphosite multiplicity of the three different enrichment methods; label-free quantitative phosphoproteome analysis of HeLa/neuron digests using variable amounts of starting material; dynamic range in the phosphoproteome can be extended by using more starting material; and linearity of the quantitative phosphopeptide enrichment by automated Fe(III)-IMAC enrichment. (PDF)

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    This article is cited by 99 publications.

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    Cite this: J. Proteome Res. 2017, 16, 2, 728–737
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