Kevin Zemaitis

Meep

Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms Spatially resolved mass spectrometry (MS)-based multiomics workflows are becoming more utilized for revealing the complex biology that occurs within tissues. However, these approaches commonly require multiple independent tissue sections to analyze the metabolite and protein compositions of these samples. This poses a significant challenge in preserving cell- or region-specific molecular fidelity, as variations between tissue sections can compromise the accurate correlation of molecular data. Here, we developed workflows for comprehensive multiomics profiling from a single tissue section (STS) using different MS modalities. We enhanced the functionality of an electrically insulated substrate by employing metal-assisted approaches that enabled both MS-based untargeted spatial metabolomics and proteomics from STS. This allowed metabolite imaging using matrix-assisted laser desorption/ionization-MS imaging (MALDI-MSI), without compromising it for subsequent proteome profiling with laser capture microdissection (LCM)-based technology. Specifically, implementing copper tape as a backing for polyethylene naphthalate (PEN) slides enabled the detection of >140 metabolites across a poplar root tissue section using MALDI-trapped ion mobility spectrometry time-of-flight (timsTOF)-MS. Afterward, we detected 6571 unique proteins from two distinct root regions by leveraging LCM technology coupled to our microdroplet based sample preparation approach. We also developed an alternative workflow utilizing gold-coated PEN substrates for imaging with MALDI-Fourier-transform ion cyclotron resonance (FTICR)-MS, which permitted the profiling of >170 metabolites and the identification of 6542 unique proteins across a single poplar root tissue section. These results were comparable to using each omics analysis independently. These approaches offer new opportunities for high-resolution molecular profiling of multiple omics levels across biological tissues.

Enhanced Spatial Proteomics and Metabolomics from a Single Tissue Section Using MALDI-MSI and LCM-microPOTS Platforms #AC pubs.acs.org/doi/10.1021/...

Was half asleep with an alarm to check on the instrument to start a new run. New run started. Cannot fall asleep, why is life cruel.

Neurotransmitters are rude.

Left achilles blew up running through an airport, I'm trying to be responsible after surgery and care about health. But then I remember 2020.. a trimalleolar ankle fracture and ligament tear with ORIF, I scooted back ASAP to finish my PhD. I didnt do PT then, and I feel guilty now taking my time.

Don't think I'm mentally prepared for 7 days of straight imaging on 12T trying to reduce downtime to 0... talk about big data, its about to be over a 15TB week

Survived both ACS Spring 2025, and the next week the DOE BSSD meeting. One poster, two talks. And now just kinda hoping I never fly again.

It was a lot of great discussion. But wow, back to back is awful missing one flight, and nearly missing two others by a minute.

a man with glasses and the words " it 's true " behind him ALT: a man with glasses and the words " it 's true " behind him

First ACS for me, and agreed.

Grant text I think I finished, and here's a little dump of bathroom progress. Top tip: never do subway tiles, they are evil. Already have been through 2000 tile spacers, maybe for a backsplash, but not an entire bathroom.

Suppose backup career for science is renos lol. Although my time of several months will not make people happy

Oh yeah... I forgot about posting these. We're now here lol. There's many developments.

Spatial top-down proteomics for the functional characterization of human kidney - Clinical Proteomics Background The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in ...

Happy to share this one, outlining our workflow developed through HuBMAP to look into proteoforms in human kidney. We found logical insight into FTU level proteoform differences in healthy samples. Moving forward, diseased tissues hold a lot of secrets!

doi.org/10.1186/s120...

This is a really fun story, and natural extension of the MIPI (metabolome informed protein imaging) pipelines Marija and Kristin started!

The more advanced the MSI, the more biology unlocked #TeamMassSpec

I'm going to be even sadder if the data was good

Found the limits of a Bruker MTPII adapter... you cannot image over the entire surface haha.

And while I'm at it here are here are some links:

doi.org/10.1128/msys...

doi.org/10.1016/j.co...

doi.org/10.1186/s130...

doi.org/10.1038/s415...

WOOHOO! 2024 is wrapped, and put into a collage.

While two papers are accepted (not in press), there's a lot of things in review, and much more cool TEAM science is coming. It's been an interesting year, with some shifted priorities.. but here's to a bright (and healthy) 2025!

As always, a little side by side for hot sauces. Valentina vs. Crystal, always so close.

Back on the oyster train, these were delightful from New Brunswick...

I'm no plumber, but in the end only one pipe leaked under pressure. Can you guess which one?

Think it's a dream of Greg's..

Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section An increasing number of spatial multiomic workflows have recently been developed. Some of these approaches have leveraged initial mass spectrometry imaging (MSI)-based spatial metabolomics to inform the region of interest (ROI) selection for downstream spatial proteomics. However, these workflows have been limited by varied substrate requirements between modalities or have required analyzing serial sections (i.e., one section per modality). To mitigate these issues, we present a new multiomic workflow that uses desorption electrospray ionization (DESI)-MSI to identify representative spatial metabolite patterns on-tissue prior to spatial proteomic analyses on the same tissue section. This workflow is demonstrated here with a model mammalian tissue (coronal rat brain section) mounted on a poly(ethylene naphthalate)-membrane slide. Initial DESI-MSI resulted in 160 annotations (SwissLipids) within the METASPACE platform (≤20% false discovery rate). A segmentation map from the annotated ion images informed the downstream ROI selection for spatial proteomics characterization from the same sample. The unspecific substrate requirements and minimal sample disruption inherent to DESI-MSI allowed for an optimized, downstream spatial proteomics assay, resulting in 3888 ± 240 to 4717 ± 48 proteins being confidently directed per ROI (200 μm × 200 μm). Finally, we demonstrate the integration of multiomic information, where we found ceramide localization to be correlated with SMPD3 abundance (ceramide synthesis protein), and we also utilized protein abundance to resolve metabolite isomeric ambiguity. Overall, the integration of DESI-MSI into the multiomic workflow allows for complementary spatial- and molecular-level information to be achieved from optimized implementations of each MS assay inherent to the workflow itself.

Single tissue untargeted multiomics? Yes, please! Our new paper is now online. @pnnl.bsky.social @bindesh1.bsky.social @imsis-americas.bsky.social
pubs.acs.org/doi/10.1021/...

To keep it rolling. Half wall is up, but in hindsight I should've checked the rough in for the toilet... whoops.

Jackhammering complete. Happy holidays everyone!

Demo is now 95% complete. Weirdly the old shower support was bags of concrete, jackhammer rental for Christmas oh jolly days!

Demo is left here for tonight, no isolation valves. Tonight we live without water until the depot opens... then demo continues.

Post Doctorate RA - Spatial Glycomics Scientist in Richland, Washington | Pacific Northwest National Laboratory PNNL is hiring a Post Doctorate RA - Spatial Glycomics Scientist in Richland, Washington. Review all of the job details and apply today!

Interested in spatial biology #TeamMassSpec? Experienced in #glycotime?

Check out this add my colleague Dušan posted for a postdoc here at PNNL. A really amazing opportunity to work with a great team, please share!

@chemjobber.bsky.social #chempostdoc

careers.pnnl.gov/jobs/10140?l...

This turned out super cool, radiata pine resin pcoket and resin canals.. just a quick look and I see several thousand molecular formula here, definitely more complex than SRFA excited to dig a bit more into this data. Wasnt exactly expecting this, but glad 7T-DESI has 1.1M RP at mz 250 #TeamMassSpec

Well. I think I may be outgrowing this computer lol, I wasn't about to wait 5 days, 8 hrs for one of three files to convert writing to external HDD. So I cleared off my SSD, and were going in hot!

I read should but an 8TB+ SSD for this computer...