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Defects in alternative splicing ofmRNA and aberrant post-translational modifications (PTMs) of a protein are shown to be important causes of disease.In MS-based Shotgun proteo-mics,proteins are enzymatically digested into peptides,separated via reversed-phase liquid chromatography (LC) and analyzed automatically by a mass spectrometer (MS).However,a major limitation of MS-based proteomics is that the connection between digested peptides and their assembly into proteins is difficult to achieve if some alternatively-spliced variants encoding a proteinare present.