Abstract
In quantitative proteomics, large lists of identified and quantified proteins are used to answer biological questions in a systemic approach. However, working with such extensive datasets can be challenging, especially when complex experimental designs are involved. Here, we demonstrate how to post-process large quantitative datasets, detect proteins of interest, and annotate the data with biological knowledge. The protocol presented can be achieved without advanced computational knowledge thanks to the user-friendly Perseus interface (available from the MaxQuant website, www.maxquant.org). Various visualization techniques facilitating the interpretation of quantitative results in complex biological systems are also highlighted.
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Acknowledgements
F.S.B. and F.S. acknowledge the support by the Norwegian Cancer Society. H.B. is supported by the Research Council of Norway.
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Aasebø, E., Berven, F.S., Selheim, F., Barsnes, H., Vaudel, M. (2016). Interpretation of Quantitative Shotgun Proteomic Data. In: Reinders, J. (eds) Proteomics in Systems Biology. Methods in Molecular Biology, vol 1394. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3341-9_19
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DOI: https://doi.org/10.1007/978-1-4939-3341-9_19
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