A system for identifying known compounds of a spectral library in a sample using a tandem mass spectrometry data independent acquisition method and automatically generating a list of related known compounds and identifying related known compounds in the sample without reanalyzing the sample using the DIA method, comprising: a separation device that separates a plurality of compounds from a sample over time; an ion source that receives the plurality of compounds from the separation device and ionizes the plurality of compounds, producing an ion beam of precursor ions; a tandem mass spectrometer that receives the ion beam and performs a DIA method by dividing a mass-to-charge ratio (m/z) range of the ion beam into two or more precursor ion mass selection windows and selecting and fragmenting the two or more precursor ion mass selection windows during each cycle of a plurality of cycles, producing a plurality of measured product ion spectra; and a processor in communication with the tandem mass spectrometer configured to (a) receive the plurality of measured product ion spectra produced from the DIA method from the tandem mass spectrometer, (b) retrieve from a spectral library of known compounds one or more product ions for each known compound, (c) compare the one or more product ions for each known compound to the measured product ion spectra to identify a compound in the sample as a first hypothesis, (d) perform a semantic search of a database of related known compounds using a name of the identified known compound, automatically generating a list of one or more matching related compounds found in the search as a second hypothesis and one or more product ions for each matching related compound, wherein the database is a database of biological pathways, protein modifications or protein functions, and wherein a matching related compound is a protein occurring with the identified known compound in a biological pathway, disease state or protein interaction network, or is a known modified form of the known compound, and (e) compare the one or more product ions for each matching related compound to the measured product ion spectra to identify one or more related compounds in the sample. a separation device that separates a plurality of compounds from a sample over time; an ion source that receives the plurality of compounds from the separation device and ionizes the plurality of compounds, producing an ion beam of precursor ions; a tandem mass spectrometer that receives the ion beam and performs a DIA method by dividing a mass-to-charge ratio (m/z) range of the ion beam into two or more precursor ion mass selection windows and selecting and fragmenting the two or more precursor ion mass selection windows during each cycle of a plurality of cycles, producing a plurality of measured product ion spectra; and a processor in communication with the tandem mass spectrometer configured to (a) receive the plurality of measured product ion spectra produced from the DIA method from the tandem mass spectrometer, (b) retrieve from a spectral library of known compounds one or more product ions for each known compound, (c) compare the one or more product ions for each known compound to the measured product ion spectra to identify a compound in the sample as a first hypothesis, (d) perform a semantic search of a database of related known compounds using a name of the identified known compound, automatically generating a list of one or more matching related compounds found in the search as a second hypothesis and one or more product ions for each matching related compound, wherein the database is a database of biological pathways, protein modifications or protein functions, and wherein a matching related compound is a protein occurring with the identified known compound in a biological pathway, disease state or protein interaction network, or is a known modified form of the known compound, and (e) compare the one or more product ions for each matching related compound to the measured product ion spectra to identify one or more related compounds in the sample. (a) receive the plurality of measured product ion spectra produced from the DIA method from the tandem mass spectrometer, (b) retrieve from a spectral library of known compounds one or more product ions for each known compound, (c) compare the one or more product ions for each known compound to the measured product ion spectra to identify a compound in the sample as a first hypothesis, (d) perform a semantic search of a database of related known compounds using a name of the identified known compound, automatically generating a list of one or more matching related compounds found in the search as a second hypothesis and one or more product ions for each matching related compound, wherein the database is a database of biological pathways, protein modifications or protein functions, and wherein a matching related compound is a protein occurring with the identified known compound in a biological pathway, disease state or protein interaction network, or is a known modified form of the known compound, and (e) compare the one or more product ions for each matching related compound to the measured product ion spectra to identify one or more related compounds in the sample.