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Shared peptides lead to reduced sensitivity for the Savitski method.A, number of identified protein groups at 1% FDR for the Savitski and MaxQuant on the Wang_base dataset. The Savitski method has sensitivity issues for highly redundant databases. B, fraction of shared and unique peptides based on in-silico digests of three databases with different levels of redundancy. For databases that include isoforms, the fraction of shared peptides is >50%. FDR, false discovery rate.
