Alternative splicing is a critical determinant of genome complexity and by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether perturbations in mRNA splicing patterns alter the composition of the proteome. We integrate RNA-sequencing (to comprehensively report intron retention, differential transcript usage and gene expression) with our recently developed data-independent acquisition (DIA) method, SWATH-MS (Sequential Window Acquisition of all THeoretical spectra – mass spectrometry), to capture an unbiased and quantitative snapshot of the impact of constitutive and alternative splicing events on the proteome. Whereas intron retention is accompanied by decreased protein abundance, alterations in differential transcript usage and gene expression alter protein abundance proportionate to transcript levels. Our findings illustrate how RNA splicing links isoform expression in the human transcriptome with proteomic diversity, and provide a foundation for studying perturbations associated with human diseases.