Lili Niu

Fantastic time at #HUPO2025 in Toronto! Congratulations to our talented Early Career researchers! Proud winners: Oeller Marc Oeller🥇 1st Place Poster, Kathrin Korff 🥈 Runner-up Poster, and @carolineweiss.bsky.social 🎤 3-Minute Thesis award! The future of #proteomics research is bright!

Scaling plasma proteomics to 6400 patients?
Hear Lili Niu at our #HUPO2025 breakfast on how 1152 samples/day and a 200 SPD Evosep Eno + Orbitrap Astral workflow quantified >400 proteins per sample.
Register: www.evosep.com/hupo2025/

1) Talk titled “High-throughput Plasma Proteomics Empowers Population-based Studies” at the @evosep.bsky.social breakfast seminar on November 10th from 8:00 - 9:00.

2) Poster about the circulating cytokine landscape in liver inflammation on November 11th from 1:15 PM - 3:15 PM ( PV.02.152)

This #hupo2025 marks the first HUPO since I became a group leader last month at Shenzhen Bay Laboratory in Shenzhen, China. I will be presenting a talk and a poster👇 Looking very much forward to connecting with old friends and meeting new ones!

If you are at HUPO 2025, catch up with our team @mannlab.bsky.social to hear about our exciting work in single-cell proteomics, immunopeptidomics, spatial proteomics, and the latest advances in mass spectrometry technology!

🎉 Congratulations to Matthias Mann on 20 years leading Proteomics & Signal Transduction at MPI of Biochemistry! Two decades of groundbreaking mass spectrometry research and training excellent future scientists.

#MS #Proteomics #Science @mannlab.bsky.social

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes. Using this resource, this study characterizes covariation of complexes, identifies mutually exclusive ...

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.

www.embopress.org/doi/full/10....

Only that the flowers look more like daisy than valerian 😂

Based on @kauralasoo.bsky.social ‘s comment about the variant also being a fine-mapped spiceQTL. I guess the “competing image” is that it’s hard to determine which MoA is truly driving the observed effect based on information we currently have.

BCAT2: 2 black cats (?) 😆

BCAT2 encoding the mitochondrial branched-chain amino acid transaminase 2, an enzyme that catalyzes BCAA catabolism.

A missense variant causing SAV Gln60Glu.

Link to the cue is that the wire connector serves as a concatenate function as cat() in R with ‘CAT’ in BCAT2 and CATabolism(?)

Ohhh I might know this one! The trait may be related to pigmentation. The SNP is a missense variant in the TYR gene, which encodes tyrosinase, an enzyme that catalyzes the first step of melanin production by converting tyrosine to dopaquinone. Link to the pun is that the car is a black convertible.

Haha, looking forward to yours

…but with a missing (NA) chair (CHR) too?

New from @mannlab.bsky.social Champions of Europe! 1200+ proteins from plasma. More of this please.

bsky.app/profile/mann...

Neat plasma from yielding 1200+ proteins from a >3000 samples study is phenomenal.. Even more phenomenal is demonstrating the feasibility of linear comparisons across samples acquired over 2.5 months of instrument time.. Awesome..

Plasma proteome variation and its genetic determinants in children and adolescents - Nature Genetics This mass spectrometry-based proteomic study profiles the plasma proteome in 2,147 children and adolescents and reveals its association with age, sex, puberty, body mass index and genetics.

Out today in Nature Genetics: Using MS-based proteomics, we mapped 1,200+ plasma proteins in 2,100+ children, showing how genetics & development shape blood protein levels during childhood.
nature.com/articles/s41588-025-02089-2
#PediatricProteomics #pQTL
First author @liliniu.bsky.social explains ⬇️

Oh it must be related to red herring 😆 a misleading clue

SLC13A2 because it’s right (red?) in front of FOXN1 and PIGS? 😂Location wise

I was looking for MSTN, Belgian Blue…

A perturbation proteomics-based foundation model for virtual cell construction https://www.biorxiv.org/content/10.1101/2025.02.07.637070v1

I hope it comes out soon… and it should

TRPM6? encodes a protein that acts as a channel for cellular and epithelial magnesium transport. Didn’t get the link to the hint though.

Inconsistent multiple testing corrections: The fallacy of using family-based error rates to make inferences about individual hypotheses During multiple testing, researchers often adjust their alpha level to control the familywise error rate for a statistical inference about a joint uni…

Not every analysis of multiple (<whatever>) requires multiplicity adjustments (correcting p-values for multiple testing):
www.sciencedirect.com/science/arti...

China’s cheap, open AI model DeepSeek thrills scientists DeepSeek-R1 performs reasoning tasks at the same level as OpenAI’s o1 — and is open for researchers to examine.

A Chinese-built large language model called DeepSeek-R1 is thrilling scientists as an affordable and open rival to ‘reasoning’ models such as OpenAI’s o1

https://go.nature.com/3WroTb1

A Technical Evaluation of Plasma Proteomics Technologies Plasma proteomic technologies are rapidly evolving and of critical importance to the field of biomedical research. Here we report a technical evaluation of six notable plasma proteomic technologies - ...

Nice review of plasma proteomics methods by Josh Coon and his group . However the perchloric acid treatment of plasma will lead to the formation of cysteic acid and methionine sulphone which is not mentioned for the DIA search. .https://www.biorxiv.org/content/10.1101/2025.01.08.632035v1