Method and apparatus for the analysis of molecules using mass spectrometry and optical spectroscopy

A method of analyzing molecules enabling chemical, structural and isomeric or conformational identification of the molecules, particularly in a stream from a chromatographic separation, comprising: generating ions from a sample of molecules to be analyzed; cooling the generated ions below ambient temperature; fragmenting at least some of the cooled ions by irradiating the ions with light at a plurality of different wavelengths (λ) within one or more predetermined spectral intervals;-recording a fragment mass spectrum of the fragmented ions comprising a detected signal (I) versus m/z over a predetermined range of m/z values for each of the plurality of different wavelengths (λ), thereby recording a two dimensional dependency of the detected signal (I) on m/z and irradiation wavelength (λ); and determining from the recorded two dimensional dependency an identity of at least one of the generated ions and/or relative abundances of different generated ions and thereby determining an identity of at least of one of the molecules and/or relative abundances of different molecules in the sample. Apparatus for performing the method is also provided.