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Mass-biased partitioning to enhance middle down proteomics analysis


Correspondence to: Catherine Fenselau, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA. E-mail:


A strategy is presented for enhancing the middle-down analysis of higher mass peptides recovered from complex protein mixtures. Following a 30-min digestion of multiple myeloma cell lysate by an acid cleavage reaction that is selective for aspartic acid, a 3000 Da membrane filter is used to bifurcate the peptide product mixture, and the heavier fraction is subjected to collisional activation with precursor selection that excludes charge states below +4. Filtration and charge state selection are shown to provide significant increases in the number of peptides identified in the mass range above 3000 Da and in information about protein sequences. Copyright © 2013 John Wiley & Sons, Ltd.