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Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in‐depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC–MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution...
For bottom‐up proteomics, there are wide variety of database‐searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid‐search approach for determining optimal database filtering criteria in shotgun...
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