Harrison Specht

When that mass spectrometry data gives Patrick vibes ...

(so sorry in advance, couldn't resist)

@jasonderks.bsky.social is presenting at iSCMS! Come by this Saturday afternoon around 2pm to hear his talk: "Increasing proteomics throughput by multiplexing in the mass and time domains".

singlecellms.org?page_id=442

don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code

use preprint servers to share your science, not advertisements

Lazy Sunday (or manic Monday depending on when you look) question to proteomics skywalkers: does/can fragpipe make mzID files for a full PRIDE dataset? Surely, right, but all I see are pep.xml.

Join us for the guest lecture of Prof. Olga Vitek olgavitek.bsky.social, leading computational mass spec expert, for cutting-edge Stats & AI insights on Sep 24, 10am, in person or
zoom. Registration: ucdavis.zoom.us/meeting/regi... #Metabolomics #AI #Massspectrometry @mikelangelipid.bsky.social

I have always been a proponent of hypothesis-free testing of metabolite rations: This paper is just great in how it takes it to the next level:

Untargeted pixel-by- pixel metabolite ratio imaging as a novel tool for biomedical discovery in mass spectrometry imaging

elifesciences.org/articles/96892

These large mass adducts will probably require different collision energies from normal peptides to create good MS2 spectra.

Try collecting a collision energy curve if you have enough sample.

Then FragPipe Open search or MaxQuant dependent peptide search.

😎 I love seeing these new, creative approaches to metalloproteomics!

A new frontier. 🧪

Riley Research Group at UW - Research The glycocode, or combinatorial patterns of glycosylation that relay biological information, functions in essential roles that govern human health and myriad diseases (e.g., cancer, infectious disease...

Really cool talk by @nmriley.bsky.social on glyco mass spec just now at the @cecamevents.bsky.social meeting on glycans in Cagliari. Check out his group’s cool work here: www.riley-research.com/research

An Underappreciated Fate of Drugs in Vivo

There’s a route that our drug molecules can take after dosing that we haven’t been paying enough attention to. Many might not even realize it exists;

New paper in @ScienceMagazine with Schoof & Porse labs: We chart early human hematopoiesis using single-cell proteomics, and amongst others developed a dynamic model linking RNA to protein levels, explaining more proteomic variation.

📄 www.science.org/doi/10.1126/...

Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).

Probabilistic scoring of DIA matches without spectral deconvolution? Not only is it possible, we're working on implementing it in Mascot DIA.

www.matrixscience.com/blog/probabi...

#proteomics #massspec

ADP-Ribosylation in Experimental Atherosclerosis: A Potential Link Between Dyslipidemia and Inflammation in Cardiovascular Disease | Arteriosclerosis, Thrombosis, and Vascular Biology

Our recent ADP-ribosylation study is now online. many #HDL proteins circulate in ribosylated forms, accumulating in plaques. This work opens a new field in dyslipidemia research! #TeamMassSpec @ahajournals.bsky.social
www.ahajournals.org/doi/10.1161/...

Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!

Human fungi-associated variants (FAVs) associate with 9 fungal taxa and overlap protein-coding genes. A Manhattan plot shows all FAVs and their associated fungal taxa at the three significance levels (exploratory, black; genome-wide, red; study-wide, blue).

What determines the human gut fungal community? @emilyvansyoc.bsky.social @erdavenport.bsky.social @symbionticism.bsky.social &co present the first #GWAS of human genetic loci that influence the abundance of gut #fungi, linking these to disease risk #mycobiome @plosbiology.org 🧪 plos.io/42bCKou

Celebrating Al Burlingame's 41 years of the @asbmb.bsky.social Molecular and Cellular Proteomics meeting which he started before "proteomics" was a term. Congrats Al!

In Praise of Weirdness

In praise of the strangeness of scientific research, which these days I think could use a few good words said for it:

🧪 Very nice feature!

Multiplexed single-cell proteomics using SCoPE2 - Nature Protocols Biological systems can now be studied at the single-cell level using mass spectrometry. In Single Cell ProtEomics (SCoPE2), a carrier sample is used to enhance peptide sequence identification with mul...

Petelski et al suggest this one: PCR plate, 384-well, standard (Thermo Fisher Scientific, cat. no. AB1384)

Passivation before using with highly pure peptides and using DDM may also help depending on input.

Happy to chat over Zoom if helpful for more ideas!

www.nature.com/articles/s41...

Big day for @neuroproteome.bsky.social All proteomic data released at neuroproteome.org and publications in print. Lots to read on AD, PD, FTD and ALS.

Moving forward to a new era: just loaded our first single cell samples from a demo on the CellenONE using Arabidopsis protoplasts. Very curious to see the results! #proteomics #singlecellproteomics #plantscience #corefacility

📣 We're excited to share the new lean-lang.org!

Relaunching our website was a key deliverable in our Year 2 roadmap to provide "improved navigation and access to valuable content, resources, and tools." We hope you like it!

#LeanLang #LeanProver

@ajbrenes.com has one for proteomics too: go.bsky.app/HH7kqEh

A portion of ye ole MS populace .. go.bsky.app/3XETWrh

We are excited to share that our Director of Proteomics Research, Dr. Sasha Singh, will be speaking at #FOGBoston at the end of this month! Registration is free for over 90% of attendees, so don't miss out! Reserve your spot at hubs.la/Q03cHRdb0. #genomics #biodata

E11 Bio is launching Volara: an open-source Python library for block-wise processing of large volumetric microscopy datasets! 🧪🔬

Volara features block-wise task abstractions, making scalable image processing more accessible, robust, and repeatable.

Read more: e11.bio/blog/volara

Ubiquitin-Proteasome System Dysregulation in Alzheimer's Disease Impacts Protein Abundance Alzheimer's disease (AD) is a relentlessly progressive, fatal neurodegenerative disorder associated with widespread aberrant proteomic changes. The full extent of protein dysfunctions in AD and their ...

The hits keep on coming from @parallelsq.bsky.social! Today we released an exciting use-case for plexDIA in single cell analysis of #alzheimer's disease, characterizing dysregulation of the 20S proteasome. #TeamMassSpec #Proteomics

www.biorxiv.org/content/10.1...

Curious about using PSMtags in your workflow? Let’s chat!
We’re working on even higher plex designs—ideas welcome

Big thanks to the Parallel Squared + MIT + CreaGen teams and everyone who helped synthesize, test, and scale this! 🙌

PSMtags - PTI - Parallel Squared Technology Institute Parallel Squared Technology Institute is a non-profit research institute that’s scaling up proteomics to illuminate the link between protein patterns, functional interactions, and disease.

🧬 All data, code, and protocols are open here: parallelsq.org/PSMtags
📂 Raw MS data: MassIVE MSV000097968
💻 Code: github.com/ParallelSquared/tag