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Mol Cell Proteomics. 2018 Mar;17(3):422-430. doi: 10.1074/mcp.RA117.000155. Epub 2017 Dec 8.

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity.

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From the ‡Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.
§Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030.
¶Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.
‖BGI-Shenzhen, Shenzhen, Guangdong 518083, China.
**Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232.
From the ‡Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030;


Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. Here we found that junction-spanning peptides are underrepresented in publicly available mass spectrometry-based shotgun proteomics data sets. Further analysis showed that evolutionarily conserved preferential nucleotide usage at exon boundaries increases the occurrence of lysine- and arginine-coding triplets at the end of exons. Because both lysine and arginine residues are cleavage sites of trypsin, the nearly exclusive use of trypsin as the protein digestion enzyme in shotgun proteomic analyses hinders the detection of junction-spanning peptides. To study the impact of enzyme selection on splice junction detectability, we performed in-silico digestion of the human proteome using six proteases. The six enzymes created a total of 161,125 detectable junctions, and only 1,029 were common across all enzyme digestions. Chymotrypsin digestion provided the largest number of detectable junctions. Our experimental results further showed that combination of a chymotrypsin-based human proteome analysis with a trypsin-based analysis increased detection of junction-spanning peptides by 37% over the trypsin-only analysis and identified over a thousand junctions that were undetectable in fully tryptic digests. Our study demonstrates that detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity, and that complementary digestion schemes will be essential to comprehensively analyze the translation of alternative splicing isoforms.

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