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J Proteomics. 2014 Jul 31;107:98-102. doi: 10.1016/j.jprot.2014.03.015. Epub 2014 Mar 26.

The proteomics quantification dilemma.

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Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany.


Proteomics is dominated today by the protein expression discourse, which favorites the bottom-up approach because of its high throughput and its high sensitivity. For quantification this proceeding is misleading, if a protein is present with more than one protein species in the sample to be analyzed. The protein speciation discourse considers this more realistic situation and affords the top-down procedures or at least a separation of the protein species in advance to identification and quantification. Today all of the top-down procedures are one order of magnitude less sensitive than the bottom-up ones. To increase sensitivity and to increase throughput are major challenges for proteomics of the next years. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.


Bottom-up proteomics; Protein species; Proteoform; Quantification; Top-down proteomics

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