This story is super awesome and the title of the blog speaks for itself! I did a little investigation of my own following the links in the blog on how the fasta for a poisonous spider species came about.. And landed on this fun read! (Behind the scenes story🤔😉) neely.github.io/FindingFASTA/ - ThreadSky

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scienthusiast.bsky.social • 40 days ago

This story is super awesome and the title of the blog speaks for itself! I did a little investigation of my own following the links in the blog on how the fasta for a poisonous spider species came about.. And landed on this fun read! (Behind the scenes story🤔😉)

https://neely.github.io/FindingFASTA/

Comments

benneely.com•40 days ago

I really need to clean up some things on the blog and add some things… but I’m really glad you dug it. The black widow was a fun use case, and like most in this game, when you least expect it an annotation will drop (that 2024, right?, paper was a surprise).

cashwood.proteaglyco.com•40 days ago

Have you or @proteomicsnews.bsky.social done a Casanovo search on the same data to see when you should de novo vs sequence?
When I analysed some Emu, there was really good overlap (but obviously no protein information to map to).

benneely.com•39 days ago

You know that’s a really good point, though in this case the DIA would’ve squashed the search, but mentioning de novo approaches as viable along with (un)related fasta is smart.

(Specific answer is de novo v database is still like 50% overlap on a good day, in my hands)

benneely.com•39 days ago

After I wrote that it made me think about early DIA days when waters had MS^all and it would make an mgf that you could search. I assume the same concept could be (is?) used for DIA de novo, right?

alisonchaves.bsky.social•39 days ago

Has anyone tried the Cascadia algorithm from Noble's Lab for de novo DIA?

cashwood.proteaglyco.com•39 days ago

I think the precursor m/z (or at least the isolation window) is mighty powerful for de novo.

scienthusiast.bsky.social•40 days ago

It is indeed like a treasure hunt, uniprot is the low hanging fruit, although I do like it for the available proteomes, but getting the unconventional proteomes fasta and to figure out the right hits is indeed fun

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