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To the Editor—Tandem mass spectrometry (MS2) data provide high-confidence molecular identification of known molecules and preliminary characterization of novel, unknown molecules (unknowns). However, for databases to be an effective resource, broad chemical space coverage is necessary. Consequently, we have created METLIN (http://metlin. scripps. edu) a highly annotated and structurally diverse database of over 850,000 molecular standards. METLIN’s tandem mass spectral library numerically covers almost 1% of PubChem’s 93 million compounds, essentially a number that can be characterized as the known chemical space. The utility of MS2 data acquisition is especially advantageous when coupled with liquid chromatography–mass spectrometry (LC–MS) analysis of complex samples 1, 2. Such datasets typically have tens of thousands of features 3, and while accurate single-stage MS …