I am listening to this great lecture by Michelle Heck, and it made me think about some other great lectures I've missed (I still have a list from lockdown). One big one I haven't tracked down is the Jimmy Eng talk at HUPO 2020 (I think @pwilmart recommended it at the time). But... I have no idea where this video is! Any help from the masses, and sorry to be lazy.

#Proteomics #teamproteome

Check me please #teamProteome: “quant” at the protein level seems normally distributed across most sample types (high and low abundance tails), but adding depth (new MS) doesn’t preserve the low abundance tail.

Is the drop off tail biologically “real”?

Ex. blood/secretome from Anderson^2 to Uhlén.

#Proteomics

I’m the late 00’s I was enamored with AFFF-MALS (or DLS), and am always surprised I am not hearing about folks using it upstream of proteomics. Could definitely work (and did for me in 2008) for EVs and likely work for some organelles and even some cell types (I don’t actually know the upper limit on size range).

Is it something Wyatt did or…?

#proteomics #teamproteome #teammassspec

Want to thank everyone here for some stellar discussion on SAAVs and searching.

Follow up: is there a SAAV-only open search option? So open-search but constrain fitting delta mass unknowns to AAs only (no funky ptms). I am off to poke around in #FragPipe but figured the crowd might know better.

#TeamMassSpec #teamProteome

https://fediscience.org/@neely/110666898318635047

Honestly, maybe this is like when I (personally) found mass spec twitter c2018: it was @educhicano pastelbiosciences and @UCDProteomics dropping links. The #teamproteome contingent is much stronger here now with a ton of heavy hitters.

I still have issues with the timeline, but at least I can get my nerd on without a limit.

Do you include Y-chromosome linked protein sequences in the analysis of samples that cannot contain them (e.g. female tissue or cell lines like HeLa, HEK-293 or MCF-7)? #teamProteome

Φ(ST) Motif diagrams for human & mouse mitogen-activated protein kinase kinase 1―MAP2K1:p―aka MEK1, MAPKK1 & PRKMK1. Three major, conserved S/T phosphodomains anchored by ΦF, RxxΦP and PxΦP acceptor motifs. #teamProteome

Probably worth a look if you are interested in this sort of thing. #teamProteome
https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00388

Φ(ST) Motif diagrams for human & mouse ubiquitin specific peptidase 5―USP5:p―has 3 discrete phosphodomains involving conserved acceptor site motifs. #teamProteome

Do you think you have as intuitive a feel for data when it is plotted with a log scale compared to the same data plotted with a linear scale? #teamProteome

Φ(ST)-motifs diagram for mouse serine/arginine-rich splicing factor 7―if I ever wrote a monograph explaining the mechanisms that give rise to the apparent complexity of ST phosphorylation patterns, this would be Fig. 1. #teamProteome

Modification diagrams for mouse cell division cycle 42, CDC42 binding protein kinase alpha & beta―CDC42:p, CDC42BPA:p, CDC42BPB:p―a small GTPase & 2 kinases that bind it. The kinase genes are paralogues & their protein PTM patterns are proteologues. #teamProteome

Modification & W-S diagram for mouse eukaryotic translation initiation factor 3 subunit H―EIF3H:p―a component of the 43S preinitiation complex with several domains that can be easily differentiated by their PTM patterns. #teamProteome

Modification diagrams for human dysferlin & myoferlin―DYSF:p & MYOF:p―ferlin family subunits where the genes are paralogues but the proteins are not proteologues. #teamProteome

Modification diagrams for human tankyrase & tankyrase binding protein―TNKS & TNKS1BP1―demonstrating contrasting attitudes towards participation in signalling cascades. #teamProteome

S/T/Y phosphorylation diagram for mouse actin-binding LIM protein 1―Ablim1:p―with known gang affiliations. #teamProteome

ω-mod diagrams for human pleckstrin homology like domain family B members 1, 2 & 3―PHLDB1:p, PHLDB2:p, PHLDB3:p―one of these things is not like the others. NB: the sequences of 1 & 2 don't overlap very much, but their PTM patterns really do rhyme. #teamProteome

Modification diagrams for human NIPSNAP1:p, NIPSNAP2:p, NIPSNAP3A:p & NIPSNAP3B:p. Small, similar mitochondrial matrix proteins of unknown function with rather blah PTMs. #teamProteome

Modification & N-linked glycosylation diagrams for human multimerin 1―MMRN1:p―lots of glycosylation, although why is one for the future. #teamProteome

Need the proteomics version of a "Field Guide to Identifying Cell Lines". #teamProteome