Protein/peptide discovery data obtained from data-dependent experiments have been used to increase the success rate of targeted quantification assays as well as automate method building. The incorporation of a quality control (QC) peptide set for discovery experiments aids the determination of relative retention times, which are stored in spectral library entries with precursor and product ion information. The inclusion of both liquid chromatography (LC) and mass spectrometry (MS) data in spectral library entries enables software programs to accurately build targeted peptide acquisition methods for large lists of peptides. The efficiency of determining the relative retention times for a set of synthetic peptides was evaluated across a number of LC–MS methods.
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