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Phil W @pwilmarth.bsky.social · 6h

Out of Sync???

Phil W @pwilmarth.bsky.social · 10h

This week's top headline from the Department of Redundancy Department: MTG says that there are a lot of weak Republican men...

Phil W @pwilmarth.bsky.social · 3d

I can't type (digital dyslexia): "They" should be "There".

Phil W @pwilmarth.bsky.social · 3d

They may be a few anti-Pho folks here in Portland but they would be hard to find on a cool rainy day. As some French lady said many, many years ago, "let them eat soup!"

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Phil W @pwilmarth.bsky.social · 3d

Disclaimer: I know nothing about the immune system. Maybe low complexity sequences don't have enough information content to distinguishing host from invader? I recall that proline-rich proteins in saliva have some low complexity peptides that fragment an ID just fine with basic proteomics methods.

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Phil W @pwilmarth.bsky.social · 4d

The great thing about standard formats is that there are SO MANY to choose from!

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Phil W @pwilmarth.bsky.social · 4d

You have to pay extra to enable the pet scan mode on Thermo Oribis...

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Phil W @pwilmarth.bsky.social · 5d

US HUPO short course topic suggestions:

You are doing it wrong because no one knows how to do it correctly.

Techniques that actually work (*extremely* short course).

AI is to science like creationism is to evolution.

Experimental designs that tell you something: finding needles in haystacks.

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Phil W @pwilmarth.bsky.social · 8d

Ha-ha. What are the project sizes? A few MB? Their combined size is probably modest. Get a 10 or 12 TB drive and archive all the old data on one drive, then put it in the desk, and you will have some top drawer data!

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Phil W @pwilmarth.bsky.social · 8d

ChatStat or StatChat??? I bet this protein is always differentially something or another: www.uniprot.org/uniprotkb/Q5...

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Phil W @pwilmarth.bsky.social · 9d

I gave a quick listen to Taylor Swift's new album. My first thought was that I hope they are not making a video for Wood...

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Phil W @pwilmarth.bsky.social · 12d

There might be a download option to include canonical plus isoforms (however, canonical and isoforms are terms that only apply to the SwissProt entries).

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Phil W @pwilmarth.bsky.social · 13d

See www.uniprot.org/help/uniprot... and www.uniprot.org/help/manual_... for more details. There is a lot of documentation at UniProt.

UniProt

UniProt is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

www.uniprot.org

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Phil W @pwilmarth.bsky.social · 13d

Isoforms are represented differently in SwissProt vs TrEMBL. Different protein forms have explicit, separate entries in TrEMBL. Those related sequences are rolled into one curated SwissProt record. There's one canonical, representative sequence and others are detailed in the record, not the FASTA.

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Phil W @pwilmarth.bsky.social · 13d

Maybe the Government shutdown means the Federal Government won't be able to terrorize "we the people" of the US as much, or are those the "essential functions" now?

Phil W @pwilmarth.bsky.social · 16d

I bet the amount of coding by folks that know nothing about coding (and have no business coding) has gone way up since AI code breakers crawled out of the swamp.

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Phil W @pwilmarth.bsky.social · 16d

There is nothing "civil" going on down here. Reporting from the war-torn Western Front...

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Phil W @pwilmarth.bsky.social · 17d

The 'ome nameome is out of control!

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Phil W @pwilmarth.bsky.social · 17d

Boy, I'm sure glad federal troops are coming to get crime under control here in Portland. On my walk today, I saw some cars not come to complete stops at stop signs. There were a few cars exceeding the speed limit. There were some pedestrians that jay walked. I saw some litter. It is out of control!

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Phil W @pwilmarth.bsky.social · 17d

The "status quome" would be easy to study...

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Phil W @pwilmarth.bsky.social · 18d

The beauty of DIA is that you make one dataset as a grad student, and you can just keep reanalyzing the same old data with each new software release until you retire! DIA really stands for data independent analysis...

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Phil W @pwilmarth.bsky.social · 18d

Good FASTA file choices are more about quality over quantity (see digitalcollections.ohsu.edu/record/3031?...). You can't do protein alternative splicing or mutations or PTMs unless you have high protein sequence coverage. You need to see what high abundance proteins are in the sample, then refine.

The effects of parsimony logic and extended parsimony clustering on protein identification and quantification in shotgun proteomics

Madhira, Raviteja

digitalcollections.ohsu.edu

Phil W @pwilmarth.bsky.social · 19d

Good question. If you search for taxon number or species, you look at the proteome options in the left sidebar at UniProt. Click on reference proteomes, then look for download options. You are looking for the phrase "one protein per gene" in a download link. I always fumble around until I find it.

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Phil W @pwilmarth.bsky.social · 19d

Canonical reference proteomes using the "one protein per gene" download option. You should have around 21K to 22K sequences for any higher eukaryotes. FASTA file choices are discussed a bit in this post: pwilmart.github.io/blog/2020/09...

Unique peptides and shotgun quantification

pwilmart.github.io

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Phil W @pwilmarth.bsky.social · 20d

Like my computer skills, I would have to be a bike mechanic at a bicycle museum. I don't think I could even get a wheel off of a new carpet fiber disco brake rodeo bike. I could probably throw ebikes in the dust bin when they break (are they even serviceable?), but they are pretty hefty...

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