Xiaojing’s paper Detection of proteome diversity resulted from alternative splicing is limited by trypsin...

Xiaojing’s paper Detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity. has been published in Molecular & Cellular Proteomics. Congratulations, Xiao Jing! 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. In this paper, we studied the proteomic coverage of exon-exon junctions in three publicly available proteomics data sets and found that trypsin preferentially cleaves exon-exon junctions and thus hinders the detection of junction-spanning peptides. This phenomenon was explained by evolutionarily conserved preferential nucleotide usage at exon boundaries according to nucleotide sequence analysis of five eukaryotic genomes. Our in silico and experimental analyses showed that complementary digestion schemes are essential to study the translation of alternative mRNA splicing to proteome diversity.