Jakub Vašíček

ProHap - Search your proteomics data against population variants! Critically important new community resource! STOP. IGNORE THE FLOWCHART ABOVE. These are bioinformatics people, they think this stuff is mandatory. I assume their conferences all have...

This new resource is AMAZING. You can easily search (re-search) your proteomics data in the context of human genomics (you know, that whole thing where we don't all have the exact same genome?) Read the paper, but instructions in the blog post - proteomicsnews.blogspot.com/2024/12/proh...

And after you've done your search, you can feed your results to this little pipeline, and it will tell you who these peptides are: github.com/ProGenNo/Pro...

Here's a flowchart overview :))

Here's an overview of how many new peptides you gain in each of the databases. If you're looking for a database best suited to Europeans, then I'd go for the 1000 Genomes European superpopulation here: zenodo.org/records/12671237 (file 240530_ProHap_EUR.tar.gz)

Thanks so much for the shout-out! That's great to see you're finding this useful!

A little note on which of the fastas to use - the HRC data we got access to was aligned with an older genome build, and many variants were lost during liftover. The 50k+ variants are in the 1000 Genomes databases.

GitHub - ProGenNo/ProHap: Proteogenomics database-generation tool for protein haplotypes and variants Proteogenomics database-generation tool for protein haplotypes and variants - ProGenNo/ProHap

Please see the GitHub project page for all relevant info on usage, availability of the databases we have created, etc.: github.com/ProGenNo/Pro...

Thanks to @lukaskall.bsky.social, @njolstad.bsky.social and other co-authors that aren't here (yet) for their contribution!

One proteome to rule them all? We have published a tool to create custom protein databases from large panels of genotypes in @naturemethods.bsky.social. Check the post below to see why it matters, why you should use it, and how it will make your life both easier and more difficult.