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YongchaoDou committed Sep 23, 2022
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[<img src="https://github.com/bzhanglab/SEPEPquant/blob/main/doc/protein-and-peptide-distribution.jpg" width=400 class="center">](https://github.com/bzhanglab/SEPEPquant)

Among the 19449 protein coding genes annotated in a RefSeq database, 14698 (75.6%) have more than one protein isoforms, and 3409 (17.5%) have 10 or more protein isoforms (Fig. 1a). Most of isoforms from the same gene have very high sequence similarity (>90%, Fig. 1b). However, among the 11809 genes with three or more protein isoforms, 6165 (52.2%) have at least one pair of isoforms with a sequence similarity lower than 90%, or an average of one amino acid difference in every 10 amino acids, suggesting the possibility to identify isoform-discriminating peptide sequences for a substantial number of genes.
To further assess the challenge and opportunities of isoform characterization using shotgun proteomics, we performed in silico trypsin digestion of the RefSeq protein database to generate fully tryptic peptides with length 7 to 50 and no missed cleavage. Among the 1,883,206 resulting peptide sequences, 2.8% could be associated to multiple genes (i.e., multi-genes peptides), 13.6% to genes with a single protein isoform (i.e., single isoform peptides), and 83.5% to genes with more than one isoforms (i.e., multi-isoforms peptides). Within the group of multi-isoforms peptides, around half could be mapped to all protein isoforms of a gene and thus providing no information for isoform discrimination (i.e., non-discriminative peptides); however, another half, or 246,615 peptides, could be uniquely mapped to one isoform (i.e., fully discriminative peptides) or a subset of isoforms (i.e., partially discriminative peptides) (Fig. 1c).


[<img src="https://github.com/bzhanglab/SEPEPquant/blob/main/doc/parsimony-selection.jpg" width=400 class="center">](https://github.com/bzhanglab/SEPEPquant)

[<img src="https://github.com/bzhanglab/SEPEPquant/blob/main/doc/sepep-quantification.jpg" width=400 class="center">](https://github.com/bzhanglab/SEPEPquant)
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