Nozomu Saeki

Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in p...

I am excited to see our performance assessment of the successor of Scanning SWATH on the Zeno TOF7600+ mass spectrometer - ZT Scan DIA - pre-printed (www.biorxiv.org/content/10.1...

A black-and-white photo shows a woman in a patterned dress with a lace collar and pearl necklace, sitting in a chair. The background features shelves with bottles and a wire basket, suggesting an early 20th-century setting, possibly a pharmacy or study.

On this day in 1879, Maud Menten was born in Port Lambton, Ontario.
In her work as a medical researcher, she became a leading expert in histochemistry and enzyme kinetics while fighting against sexism in her field.
Let's learn more about her life!

🧵1/10

Our genome encodes > 7000 microproteins that have been previously ignored in genome annotations. How do these microproteins impact tissue function? Here, we use an in vivo single-cell CRISPR screen to systematically explore microprotein function in the mouse epidermis. 1/9

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-ba...

#Microproteins may be the next frontier in #proteomics. But figuring out the publications can be tough.

If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder!

🧬 💻
#genomics
#RNASky

bit.ly/4bgJSDm

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment https://www.biorxiv.org/content/10.1101/2025.02.19.639069v1

Comprehensive discovery and functional characterization of the noncanonical proteome - Cell Research Cell Research - Comprehensive discovery and functional characterization of the noncanonical proteome

Sometimes the #microprotein field needs to police itself.

I rarely see the point in sharing disapproval for published papers. Let bygones be bygones, I suppose.

Several days ago, however, a new paper came out. My assessment is that it is bogus.

#genomics
🧬 💻

1/

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

Can a function grow gradually?
rdcu.be/d5vRC

a man in a suit and bow tie is sitting at a desk with his arms outstretched in front of a globe . ALT: a man in a suit and bow tie is sitting at a desk with his arms outstretched in front of a globe .

He said he realized that the protein didn’t do anything.

The RNAs evolved to regulate themselves in an appropriate way, taking advantage of a protein whose structure changed depending on the cellular iron status.

22/n

a cartoon says hey everybody an old man 's talking while bart simpson looks on ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on

Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight

Excited to share our review article "Finding functional microproteins", published in @TrendsGenetics. It was fun writing it together with Alex and @FeiyueYang1 in the lab. #microprotein authors.elsevier.com/a/1kNCscQbJB...

Methods: a call for papers The journal GENETICS is calling for submission of papers for a Special Issue on Experimental and Computational Methods.

"GENETICS, the flagship journal of the Genetics Society of America, is calling for papers for a Special Issue on Experimental & Computational Methods."

Eds: Stan Fields (UW Seattle), Maria Chikina (U Pittsburgh), Konrad Lohse (U Edinburgh).

Deadline Mar 1, 2025.

click.skem1.com/click/bbu3-2...

Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of s...

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

Register by Dec. 17 (11:59pm MST) for the Microproteins conference and save $200! Join organizer @thomasmartinez.bsky.social, Keynote Speaker @Jonathan W. Yewdell, and other experts to explore microproteins' roles in health and disease in Massachusetts! keysym.us/KSMicroprote... #KSMicroproteins25

A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor Reduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones...

Can a single small molecule rescue the stability of nearly all mutations in a protein?
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins A major scientific drive is to characterize the protein-coding genome as it provides the primary basis for the study of human health. But the fundamental question remains: what has been missed in prio...

#Proteomics must be one of the few fields where people still think that a long list of authors & the phrase "high-quality" will boost the credibility of a phenomenon that has been well-known (& ignored) for years. doi.org/10.1101/2024...

A researcher on a boardwalk in a DANK hawaiian forest on Molokai.

RP PLS! Iʻm hiring 3 postdocs at U Hawaiʻi to study yeast diversity and evolution, marine fungi, and the genomics of microbiomes in experimental foodwebs. All of these projects have existing datasets and LATITUDE to pursue individual interests and "blue sky" ideas www.dropbox.com/scl/fi/5d7u4...

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

Do you want to go further with your proteomics? Looking for something new in cancer?

Check out microproteins!

Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social

www.science.org/content/arti...

🔎 microprotein
🧬 💻

Figure 4. Position and type of fluorescent tag affect protein expression and P-body numbers in vivo.

The dark side of fluorescent protein tagging: the impact of protein tags on biomolecular condensation
www.biorxiv.org/content/10.1...

Wonderful tools for Ribosome profiling (Ribo-seq) within a web browser. Check out riboseq.org and academic.oup.com/nar/advance-... 🧪 #RNASky #ribosome

🧪 #AcademicSky #AcademicJobs #SciJobs #ScienceJobs #STEMJobs #FacultyPosition

High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue Formalin-fixed paraffin-embedded FFPE patient tissues are a valuable resource for proteomic studies with the potential to associate the derived molecular insights with clinical outcomes. Here we prese...

Once upon a time, FFPE was considered a death knell for studying molecular biology in archived cancer samples.

So many wonderful advances in this area now make FFPE a rich source for study of RNA, DNA and protein.

Check out this new gem. 💎

#proteomics
#genomics

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

thank you!

Hi, would it be alright if I joined this community? Thank you.

We will feature many of your favorite BlueSky scientists!

@carvunis.bsky.social
@thomasmartinez.bsky.social
@sebastiaanvheesch.bsky.social
@microproteins.bsky.social
@nickywhiffin.bsky.social
@uweohler.bsky.social
@luispedrocoelho.bsky.social
@slavofflab.bsky.social

Than you!

Do you mind if I join?

News in Proteomics Research | Astral vs TIMSTOF Ultra on real single cells? Just about evenly unreal numbers! proteomicsnews.blogs...

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#proteomics #prot-other

Extensive binding of uncharacterized human transcription factors to genomic dark matter Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...

(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....

Alternate RNA decoding results in stable and abundant proteins in mammals Amino acid substitutions may substantially alter protein stability and function, but the contribution of substitutions arising from alternate translation (deviations from the genetic code) is unknown....

We report many proteins not predicted by the genetic code.
They are stable & abundant O( 10³ ) copies / cell.

Generative mechanisms include codon-anticodon mismatches & RNA modifications.

Their abundance depends on codon frequency & protein stability.

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

We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...