The identification, quantitation and global characterisation of all proteins within a given proteome are extremely challenging. This is due to the absolute detection limits of technology as well as the dynamic range in expression of proteins; and the extreme diversity and heterogeneity of the proteome. To overcome such issues, the use of separation technologies has played a critical role in reducing sample complexity. To date, a plethora of chromatographic and electrophoretic fractionation tools have evolved over the years assisting in simplifying complex protein and peptide mixtures. Here, we review a range of these technologies highlighting the challenges of protein and peptide analysis in the context of proteome research and some of the advantages and disadvantages of present techniques.
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