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The relevance of libraries of annotated MS/MS spectra is growing with the amount of proteomic data generated in high‐throughput experiments. These reference libraries provide a fast and accurate way to identify newly acquired MS/MS spectra. In the context of multiple hypotheses testing, the control of the number of false‐positive identifications expected in the final result list by means of the calculation...
Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein mixtures have so far been using MS‐based shotgun proteomics. The standard approach...
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