Tim Cummins

Multi-region spatial transcriptomics reveals region specific differences in response to amyloid beta (Aβ) plaque induced changes in Alzheimer's disease (AD) - PubMed Our results demonstrate the value of simultaneously profiling AD-omic and spatial modalities in multiple regions to elucidate how cortical region-specific differences contribute to selective vulnerability and resilience during neurodegeneration. These cortical region and Aβ microenvironment-specific …

New publication by our student, Odmaa Bayaraa: 'Multi-region #SpatialTranscriptomics reveals region specific differences in response to amyloid beta (Aβ) plaque induced changes in #Alzheimers disease (#AD)'

So proud of this work and of Odmaa! Check it out 🧬🧠
pubmed.ncbi.nlm.nih.gov/41318546/

Oh goodness 😆

Cool, we have plasma and serum in the lab and admix pools for each experiment especially when trying to determine batch effects. Depletion is interesting, several papers on how this affects plasma proteome.

The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells - Communications Biology A review of recent innovations driving low-input phosphoproteomics, focusing on miniaturized workflows, multiplexed labelling, automated enrichment, and advanced acquisition methods for scarce biologi...

www.nature.com/articles/s42...

Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics In BriefOptimization of experimental parameters for automated on-bead phosphoproteomics sample preparation for low-input samples was conducted. Key factors assessed included glycolic acid concentratio...

www.mcponline.org/article/S153...

Who won the FIFA prize for medicine this year? 🤣🤦

FIFA, nothing tangentially corrupt going on in this organization HAHA!

Yeah, Astral alone eats up a nice chunk of that! Nice setup! We've installed a CellenONE X1 Neo this year. Excited to see how it can power up single cell work.

Nothing like a good snow in Kentucky to make it feel festive!

Speed it up; Mr. mass spectrometer haha! Or is it Dr. mass spectrometer :)

#RenalPath: Diffuse granular capillary wall staining for phospholipase A2 receptor (PLA2R). PLA2R staining is positive in approximately 70% of patients with clinically idiopathic membranous nephropathy (immunofluorescence microscopy, PLA2R).

bit.ly/2xVkJzs (FREE)

Highly skilled surgeons, cardiologists, pulmonologists and nephrologists have saved my wife, my daughter, my brother and my dad with their dedication to learning about the human condition at the most detailed level. These people we need, and they come from all over the world.

It’s always good to go back to the lab and see how the lab coat fits the day after Thanksgiving. Also, data is to be had woohoo!

Not some kind of psychology test… single cell maps eek

Someone is a psychopath pipet tipping like such…

Very nice!

Neuronal Proteins as Antigenic Targets in Membranous Nephropathy Abstract. Context: The discovery of new target antigens in membranous nephropathy (MN) has revealed new disease phenotypes and, in some cases, has suggested mechanisms of disease shared by two concurr...

Neuronal proteins show up in so many of our proteomics and mass spectrometry experiments on renal tissues and cells, especially the podocyte! Larry Beck and Laith Al-Rabadi discuss this in the context of MN here.

Antigens in membranous nephropathy: discovery and clinical implications | Nature Reviews Nephrology Membranous nephropathy is an autoimmune disease that results in an accumulation of antigen–antibody (IgG) immune complexes along the subepithelial region of the glomerular basement membrane and is the most common cause of nephrotic syndrome in adults. The diagnosis of membranous nephropathy is based on the presence of granular IgG on immunofluorescence microscopy and subepithelial electron dense deposits along the glomerular basement membrane on electron microscopy. Prior to 2009, the target antigen within the immune complexes was unknown. However, in the past 15 years, and in particular the past 5 years, several target antigens have been identified. These target antigens include PLA2R, THSD7A, EXT1 and EXT2, NELL1, SEMA3B, NCAM1, CNTN1, HTRA1, FAT1, PCDH7, NTNG1, PCSK6, NDNF and MPO. Several rare putative antigens have also been reported. These findings have transformed our understanding of membranous nephropathy from that of an idiopathic disease, which results from an autoimmune res

Discoveries in antigens for membranous nephropathy, a top nephrotic syndrome cause, expand diagnosis & treatment potentials. PMID:40691733, Nat Rev Nephrol 2025, @NatRevNeph https://doi.org/10.1038/s41581-025-00980-z #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

Also HTRA1 in 2022 from Larry Beck and Laith al Rabadi.

Definitely changed the field — 2009 was a good year for iMN w/ good mass spec tools (i.e, linear ion trap gasp!) — much progress being made. My favorite was SEMA3B in pediatric MN, gave grand rounds on this a couple years ago.

The UofL contingent proteomics crew spanning 25 yrs and all kinds of areas of mass spectrometry. Staff Excellence Awards!

YouTube video by Parallel Squared Technology Institute Increasing Mass spectrometry throughput using time encoded sample multiplexing | Jason Derks

Parallelized LC-MS analysis to multiplex and allow 100 samples per day! Essentially — a 3 column separation at 3 time points then merged to emit into the same detector at offset retention times. Analyzing the data is the complicated part; they solved that too! Very cool method.

EVEN more interesting is; I didn't need a massive Bioinformatics team to come to those conclusions! Ha!

Ironic (maybe I'm using this the wrong way) to see someone shrug off my findings at a meeting as yeah well that is pretty expected... then find they published the exact same thing within a week in the title of the paper! I guess they wanted me to tell them the novel things they missed ;)

LOL

2-dimensional LC is the fairest way to cheat on the front end and get spatially resolved peptides. How do glycosylated species fair in this context? Does ETD help?

Fair cheating is the key :)

The oldest instrument (linear ion trap) in the lab is less sensitive than the newest and greatest shiny orbitrap, yet the old instrument has yielded some of the best results thus far. Sample prep is the key. Zeroed in FWHM doesn't overcome bad samples. Speed-accuracy-sample prep, which is the key?

My nephew’s dream was to become a firefighter and save lives. He never thought he would be responding to an airliner crash in our hometown. Amazing kid — if ever I need help, I can call him for anything.

#KidneyWeek 2025 Houston. Podocyte injury and nephrotic syndrome proteomics was very popular with lots of discussion and interactions. SRNS, SSNS.

Astros World Series. Rustic lunch.

#KidneyWeek Houston. One of the best in terms of collegial interactions and discussions. Spending time thinking about better ways to answer kidney related questions, with a mass spectrometer, of course ;)