Alternative splice isoform companion data on website
We recently published our study on finding protein alternative isoforms in the human proteome (https://www.ncbi.nlm.nih.gov/pubmed/31825849). The paper describes a method that uses RNA sequencing data to compile a list of alternative splice sites in a human tissue, then translating the data into protein sequences to re-analyze mass spectrometry data. We reprocessed over 80 million mass spectra on ProteomeXchange and found over 1,000 non-canonical protein isoforms, including a couple hundred peptides that were not previously documented in popular protein sequence databases.
Alternative Splicing Transcripts Translated as Proteins
The results show that not only are more alternative splicing isoforms translated into proteins than previously analyzed, many are tissue-specific and can influence protein functions through excising known protein-protein interaction and post-translational modification sites.
We have now created a new section on our website that hosts a web app for interactive data analysis. With the app, users will be able to search each analyzed tissue to display the identified non-canonical peptide sequences as well as the Uniprot ID of the canonical proteins they belong to. Some new data including two new tissues that have been analyzed since the paper was published have also been uploaded to the growing dataset (heart, liver, lung, adrenal gland, pancreas, colon, ovary, testis, thyroid, esophagus, prostate, thyroid, stomach, uterus). We think this can be a useful tool to keep track of the growing list of translated alternative splicing sequences in the human proteome!
Feel free to browse and download the dataset through the top navigation bar under Data & Tools > Splice Isoform Dataset, or directly through this link here http://maggielab.org/data_splice and let us know what you think!