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In recent years the inherit problems of the traditional data-dependent acquisition mode in shotgun proteomics have been recognized. These include bias towards fragmentation of abundant peptides, stochastic effects and chimeric product ion spectra. One of the approaches to deal with these limitations is by a technique termed data-independent acquisition (DIA). This technique is comprised of several approaches, all of which relate to the parallel fragmentation of peptides in an unbiased manner, irrespective of their abundance. Presented here is one such approach termed MSE. This chapter discusses the performance from this unique acquisition mode for identification and quantification of proteins in complex biological samples.

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