Analytic framework for peptidomics applied to large-scale neuropeptide identification

Anna Secher, Christian D. Kelstrup, Kilian W. Conde-Frieboes, Charles Pyke, Kirsten Raun, Birgitte S. Wulff and Jesper V. Olsen ()
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Anna Secher: Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
Christian D. Kelstrup: Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
Kilian W. Conde-Frieboes: Protein & Peptide Chemistry, Novo Nordisk A/S
Charles Pyke: Histology and Imaging, Novo Nordisk A/S
Kirsten Raun: Incretin & Obesity Pharmacology, Novo Nordisk A/S
Birgitte S. Wulff: Incretin & Obesity Research, Novo Nordisk A/S
Jesper V. Olsen: Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: Abstract Large-scale mass spectrometry-based peptidomics for drug discovery is relatively unexplored because of challenges in peptide degradation and identification following tissue extraction. Here we present a streamlined analytical pipeline for large-scale peptidomics. We developed an optimized sample preparation protocol to achieve fast, reproducible and effective extraction of endogenous peptides from sub-dissected organs such as the brain, while diminishing unspecific protease activity. Each peptidome sample was analysed by high-resolution tandem mass spectrometry and the resulting data set was integrated with publically available databases. We developed and applied an algorithm that reduces the peptide complexity for identification of biologically relevant peptides. The developed pipeline was applied to rat hypothalamus and identifies thousands of neuropeptides and their post-translational modifications, which is combined in a resource format for visualization, qualitative and quantitative analyses.

Date: 2016
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DOI: 10.1038/ncomms11436

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