Harrison Specht
@harrisons.bsky.social
880 followers 490 following 72 posts
Exploring biology with mass spectrometry
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Reposted by Harrison Specht
willfondrie.com
I'm a huge fan of this proposal!

If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data?

pubs.acs.org/doi/10.1021/...
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.
pubs.acs.org
Reposted by Harrison Specht
parallelsq.bsky.social
Throwback Thursday continues with a presentation by Maddy Yeh and Mark Adamo from Research Fest: "Tags for improving peptide sequencing and throughput in sensitive proteomics".

Watch on YouTube: www.youtube.com/watch?v=jA2I...
Tags for improving peptide sequencing and throughput in sensitive proteomics | Maddy Yeh, Mark Adamo
YouTube video by Parallel Squared Technology Institute
www.youtube.com
Reposted by Harrison Specht
Reposted by Harrison Specht
carlzimmer.com
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
harrisons.bsky.social
When that mass spectrometry data gives Patrick vibes ...

(so sorry in advance, couldn't resist)
Reposted by Harrison Specht
parallelsq.bsky.social
@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
Conference Program – iSCMS
singlecellms.org
Reposted by Harrison Specht
skyjase.bsky.social
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
Reposted by Harrison Specht
benneely.com
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.
Reposted by Harrison Specht
metabolomics-wcmc.bsky.social
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
Reposted by Harrison Specht
ksuhre.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
harrisons.bsky.social
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.
harrisons.bsky.social
😎 I love seeing these new, creative approaches to metalloproteomics!

A new frontier. 🧪
pride-ebi.bsky.social
PXD056024 🚨

New metalloproteomics method based on three dimensions of liquid chromatography hyphenated with inductively coupled sector-field mass spectrometry

🚨 New dataset alert! 🚨
Reposted by Harrison Specht
dereklowe.bsky.social
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;
An Underappreciated Fate of Drugs in Vivo
www.science.org
Reposted by Harrison Specht
fabiantheis.bsky.social
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/...
Reposted by Harrison Specht
matrixscience.bsky.social
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
Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).
Reposted by Harrison Specht
Reposted by Harrison Specht
lindsaykpino.com
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!
Reposted by Harrison Specht
plosbiology.org
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
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).
Reposted by Harrison Specht
samyers-lab.bsky.social
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!
Reposted by Harrison Specht
dereklowe.bsky.social
In praise of the strangeness of scientific research, which these days I think could use a few good words said for it:
In Praise of Weirdness
www.science.org
harrisons.bsky.social
🧪 Very nice feature!
drandreahoward.bsky.social
I don’t know who needs this right now, but I really enjoy browsing “Paper Skygest”, a feed of posts on academic papers *from people you follow*. I think it’s what a lot of us are actually here for
harrisons.bsky.social
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...
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...
www.nature.com
Reposted by Harrison Specht
winchesterl.bsky.social
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.