ronbeavis.bsky.social
Doing science for money since 1981.
Putting it online since 1995.
Does not engage in cancer research.
QA >> QC
I enjoy doing things I am not very good at doing.
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Any suggestions of a good place to start reading?
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Very true but normally that is associated with intracellular membrane bound compartments, like endosomes or worn out mitochondria. I can't find any discussion of their being used that way wrt the cell membrane, though.
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IDS:p may pick up N-linked hitchhikers at 3 acceptors on its wild ride through the ER, for unknown reasons. Also shown: what the heck L-Iduronate 2-sulfate looks like.
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FUCA1:p does manage to pick up some N-linked glycosylation itself on its journey, but it probably doesn't last long once the lysosome's pH drops as it ramps up for its "suicide bag" destiny.
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There still seem to be the same problems that have been present since the '00s. No 2 labs use the same workflow, so any LIMS has to be very configurable: a lot of internal complexity & tricky configuration API. The small market also leads to high yearly fees (if you want to stay in business).
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For those who have forgotten, PTMs can be less sparingly used in other cellular compartments.
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It is almost nice (in a schadenfreude sort of way) to see that time has not had any effect on this particular problem. The "generalized proteomics LIMS system" may simply not be possible.
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The fact that these guys could look back at ML-based conclusions & show which ones were obviously faulty is pretty well the whole point of publishing― a feature rather than a bug.
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Is "crisis" the right language? If you think the "literature" is a big bag of true facts, then maybe. But if you view it as a bunch of proposed, but usually faulty, explanations for observed reality, then not so much.
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Private banks still run the show in Canada & they are never going to agree to cede any piece of their markets to a crown corporation.
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I currently use this idea to divide up a protein's occupied (obs) S/T acceptors into clades based on the adjacent residues (± 6 aa) to guess how many kinases would be needed to do the job. For the example acceptor below (TRIM3:p), it's clade would be "+4φ0".
…VKRRVKφPGGPGS…
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Their labour costs are actually down year over year, those "losses" are just creative accounting where investments and equity on their balance sheets are being misrepresented. Expanding services and changing management is where it's at.
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SGSH:p picks up at least 3 N-linked glysosylations on its wild ride through the ER and Golgi, but how long do they last in its forever home in the lysosome?
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HEXA:p does have at least one N-linked glycosylation acceptor that is occupied during its passage through the endoplasmic reticulum & Golgi apparatus.
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It is particularly puzzling, given that Carney was an ADM in Finance for 3 years under Ministers Goodale & Flaherty. He knows more about how the nuts & bolts of the budgetary process works than most previous PMs.
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It also has at least 3 confirmed N-linked glycosylation acceptors that are occupied, at least for some fraction of this protein's life cycle.
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For the MS-pendants in the crowd, the fully tryptic peptide containing the intact D205-T206 bond is also easily (although rarely) observable using bottom-up/shotgun methods.
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At some point in its journey, AGA:p acquires 2 N-linked glycosylations, I would assume ironically. It also requires cleavage at D205-T206 to become active.
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