A method for analysing tandem or multi-stage, MS n, mass spectral data (200, 301) of a substance, the method comprising: identifying a plurality of candidate chemical structure sets for the substance, each set being identified using one or more respective properties of the mass spectral data (200, 301), wherein identifying the plurality of candidate chemical structure sets comprises identifying: a candidate chemical structure set (210a, 210b, 303) by searching a mass spectral library comprising chemical structure representations of characterised chemicals and respective mass spectral library data; and a candidate chemical structure set (210a, 210b, 306) by searching a chemical structure library; identifying a plurality of groups of candidate chemical structures, each group of candidate chemical structures comprising one candidate chemical structure from each candidate chemical structure set; and determining a level of similarity between candidate chemical structures from different candidate chemical structure sets for each of the plurality of groups of candidate chemical structures, so as to determine a likelihood that one of the candidate chemical structures represents the substance; wherein searching the mass spectral library comprises: identifying a peak group in the mass spectral data (200, 301), the peak group comprising peak group data, wherein the peak group comprises a tandem or multi-stage, MS n, mass spectrum; and identifying a characterised chemical in the mass spectral library as a candidate chemical structure when the identified peak group data corresponds with mass spectral library data of the characterised chemical; and wherein searching the chemical structure library comprises: identifying a peak in the mass spectral data (200, 301) and a respective mass-to-charge ratio; and identifying a chemical structure in the chemical structure library as a candidate chemical structure when a mass -to-charge ratio of the chemical structure in the chemical structure library corresponds with the mass-to-charge ratio of the identified peak. identifying a plurality of candidate chemical structure sets for the substance, each set being identified using one or more respective properties of the mass spectral data (200, 301), wherein identifying the plurality of candidate chemical structure sets comprises identifying: a candidate chemical structure set (210a, 210b, 303) by searching a mass spectral library comprising chemical structure representations of characterised chemicals and respective mass spectral library data; and a candidate chemical structure set (210a, 210b, 306) by searching a chemical structure library; identifying a plurality of groups of candidate chemical structures, each group of candidate chemical structures comprising one candidate chemical structure from each candidate chemical structure set; and determining a level of similarity between candidate chemical structures from different candidate chemical structure sets for each of the plurality of groups of candidate chemical structures, so as to determine a likelihood that one of the candidate chemical structures represents the substance; wherein searching the mass spectral library comprises: identifying a peak group in the mass spectral data (200, 301), the peak group comprising peak group data, wherein the peak group comprises a tandem or multi-stage, MS n, mass spectrum; and identifying a characterised chemical in the mass spectral library as a candidate chemical structure when the identified peak group data corresponds with mass spectral library data of the characterised chemical; and identifying a peak group in the mass spectral data (200, 301), the peak group comprising peak group data, wherein the peak group comprises a tandem or multi-stage, MS n, mass spectrum; and identifying a characterised chemical in the mass spectral library as a candidate chemical structure when the identified peak group data corresponds with mass spectral library data of the characterised chemical; and wherein searching the chemical structure library comprises: identifying a peak in the mass spectral data (200, 301) and a respective mass-to-charge ratio; and identifying a chemical structure in the chemical structure library as a candidate chemical structure when a mass -to-charge ratio of the chemical structure in the chemical structure library corresponds with the mass-to-charge ratio of the identified peak. identifying a peak in the mass spectral data (200, 301) and a respective mass-to-charge ratio; and identifying a chemical structure in the chemical structure library as a candidate chemical structure when a mass -to-charge ratio of the chemical structure in the chemical structure library corresponds with the mass-to-charge ratio of the identified peak.