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.
Quantification Data interpretation Perseus Data post-processing
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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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