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[00578] In a first set of embodiments of the method according to the fifth aspect, the fractionated digested peptides are obtained by preparing the biological sample to obtain a processed biological sample comprising solubilized proteins to be used in the protein analysis, fractionating the processed biological sample to obtain a solubilized protein fraction comprising the solubilized proteins from the sample, digesting the solubilized proteins from the sample with a site specific proteolytic enzyme to obtain digested solubilized proteins from the sample, and fractionating the digested solubilized proteins to obtain fractionated digested peptides from the digested solubilized proteins from the biological sample
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