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In NMR and IR, different functional groups are distinguishable by characteristic chemical shifts and wavenumbers and identical functional groups with differing neighboring substituents still give distinguishable signals. Mass spectra, unlike NMR and IR spectra, have no frame of reference. Each fragment mass has to be interpreted in the context of other masses.
Dr. Daniel L. Sweeney, author of "Mass Spectrometry by the Numbers"(available on Amazon), is a mass spectrometrist who believes that fragmentation
data should be interpreted by viewing small molecules as mathematical
partitions of the molecular weight. Partitioning allows fragment masses to be interpreted in the context of other masses in the spectrum. Dan has been doing LCMS and
interpreting MS/MS data for thirty years.
Dan also consults on mass spectral interpretation.