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The most important step in any quantitative proteomic pipeline is feature detection (aka peak picking). However, generating quality hand-annotated data sets to validate the algorithms, especially for lower abundance peaks, is nearly impossible. An alternative for creating gold standard data is to simulate it with features closely mimicking real data.
(Noyce et al., 2013) Mspire-Simulator: LC-MS shotgun proteomic simulator for creating realistic gold standard data. J Proteome Res.