Core Skills in Cardiovascular Research | AJP-HEART <p>The <em>American Journal of Physiology-Heart and Circulatory Physiology</em> publishes original investigations on the physiology of the heart, blood vessels, and lymphatics, including experimental ...

A reminder that we have a very special call for paper at AJP Heart Circ on "Core Skills in Cardiovascular Research". We are looking to highlight core competencies, methodologies, and career skills in cardiovascular research. All types of articles are welcome! journals.physiology.org/journal/ajph...

Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture Alamillo et al. present a D2O labeling mass spectrometry method to measure protein turnover rates that is compatible with multiple cell cultures and medium formulations. The method reveals a parsimoni...

Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture: Cell Reports Methods www.cell.com/cell-reports...

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search www.nature.com/artic...

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#proteomics #prot-paper

Establishing a Top-Down Proteomics Platform on a Time-of-Flight Instrument with Electron-Activated Dissociation Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications; thus, there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTM’s site localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system.

New manuscript from the lab to establish a Top Down MS platform using electron activated dissociation on the Sciex ZenoTOF 7600 is out at the Journal of Proteome Research!

pubs.acs.org/doi/full/10....

Celebrate International Women's Day by reading the Special Issue of the Journal of Proteome Research, highlighting the essential contributions women scientists have made—and continue to make—in the fields of Proteomics and Metabolomics. ow.ly/eBcV50TWOpV #InternationalWomensDay 🧪

Proteomic diversity in bacteria: Insights and implications for bacterial identification Mass spectrometry-based proteomics has revolutionized bacterial identification and elucidated many molecular mechanisms underlying bacterial growth, c…

🧵(1/7) Our first 🦋 post is nothing less than:

🚀 New Research Paper Alert! 🚀

🦠 Big news for #Bacterial #MassSpec #Proteomics!

2025 has started properly for our team. 🥳

Nucleic Acids Research has arrived on Bluesky! Follow them for the latest on biology and biochemistry of nucleic acids and proteins with which they interact. Run by scientists for scientists and a pioneer in Open Access. @narjournal.bsky.social

C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.

Cells are filled with toxic stuff that damages healthy proteins. Is that garbage just left to rot on the curb? No way! Ubiquitin ligases have evolved to recognize chemical damage and clean it up! www.nature.com/articles/s41...

A temperature-inducible protein module for control of mammalian cell fate - Nature Methods The Melt (Membrane localization using temperature) protein translocates to the plasma membrane upon temperature shift. Melt variants with a range of switching temperatures enable straightforward therm...

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

This is 💥 💥💥💥💥

In the present discussions about NIH and the need for reform, two recurring points I am seeing are:

(1) NIH doesn't fund truly high impact research

(2) NIH needs to experiment with alternative approaches to peer review, particularly for high risk-high impact research

1/n

Welcome immigrants from X interested in science to the friendlier skies of @bsky.app, as documented by a new @nature.com survey (but you already knew that 😉)
"Bluesky is much better for science. There is much less toxicity, misinformation, and distractions."
www.nature.com/articles/d41...

Now online - the Feature Review "Protein N-terminal modifications: molecular machineries and biological implications" from @natmachinery.bsky.social and colleagues.

#Acetylation #Methylation #Myristoylation #Ubiquitylation #Oxidation #Arinylation

authors.elsevier.com/sd/article/S...

A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research - Communications Biology Longitudinal proteomics study identifies variability in proteome alterations in different tissues, reveals distinct consensus semitryptic motives in different organs and provides criteria for designin...

Longitudinal proteomics study identifies variability in proteome alterations in different tissues, reveals distinct consensus semi-tryptic motives in different organs and provides criteria for designing proteomic studies involving post-mortem samples.

www.nature.com/articles/s42...

The Mann lab is here now, be sure to follow them.

Also the Bluesky proteomics migration is almost complete!

Chemical tools to define and manipulate interferon-inducible Ubl protease USP18 - Nature Communications USP18 is a multifunctional cysteine protease involved in IFN pathways. Here, the authors report chemical probes and chemoproteomics platforms that allow to detect and perturb USP18 activity in complex...

Happy to share our work published www.nature.com/articles/s41.... We describe the design of activity-based probes and chemoproteomic strategies to study USP18.

A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research - Communications Biology Longitudinal proteomics study identifies variability in proteome alterations in different tissues, reveals distinct consensus semitryptic motives in different organs and provides criteria for designin...

I am excited to share our latest paper on post-mortem multi-organ protein changes in a clinically relevant mouse model! www.nature.com/articles/s42...

A huge shoutout to my amazing co-authors for their incredible contributions!

Key highlights in replies (1/n)

May Institute on Computation and Statistics for Mass Spectrometry and Proteomics @KhouryCollege @Northeastern in Boston MA is happening in person on April 28-May 11, 2025 and is accepting applications! You will not regret attending computationalproteomics.khoury.northeastern.edu

(J Proteom) Molecular insights into myelomeningocele via proteomic analysis of amniotic fluid: Publication date: Available online 6 January 2025

Source: Journal of Proteomics

Author(s): Lucie Guilbaud, Kévin Roger, Andree Schmidt, Cerina Chhuon, Stephan… http://dlvr.it/THCC1G #MassSpecRSS

Mass spec proteomics to identify the source of proteinaceous fibers in a textile material from about 1200 years ago!!!

"...with the peptide sequences measured confirming the presence of South American camelids, most likely llama or alpaca."

(Acc Chem Res) [ASAP] Mass Spectrometry-Based Protein Footprinting for Protein Structure Characterization: Accounts of Chemical ResearchDOI: 10.1021/acs.accounts.4c00545 http://dlvr.it/THCbcr #MassSpecRSS

Plasma proteomic signatures of social isolation and loneliness associated with morbidity and mortality - Nature Human Behaviour Shen et al. characterize protein signatures in the blood associated with social isolation and loneliness, demonstrating how these link social isolation and loneliness to an increased risk of disease…

Plasma proteomic signature related to social isolation or loneliness is associated with the incidence of five diseases and mortality. - Nature Human Behaviour

Global organelle profiling reveals subcellular localization and remodeling at proteome scale Organelle proteomics defines the cellular landscape of protein localization and highlights the role of subcellular remodeling in driving responses to perturbations such as viral infections.

Fantastic work by my Biohub colleague Manu Leonetti and his amazing team published in #Cell! 🧪

Human cell #proteomics subcellular landscape and its dynamic remodeling using #organelle IP.

Paper here www.cell.com/cell/fulltex...
Explore the date organelles.czbiohub.org

Congratulations to the team

(Top) Schematic representation of Fus1opto used to block cells pre-fusion in the dark and synchronize fusion upon blue light exposure. (Bottom) Time-lapse movie of h90 fus1opto cells mated in the dark and exposed to blue light at t = 0’, where Fus1C-CRY2 is tagged with sfGFP and cytosolic mTagBFP2 is expressed from the P-cell specific map3 promoter.

Nitrogen-starvation of #FissionYeast inactivates growth pathways (incl TORC1) & can trigger sexual reproduction. @sophiemartinlab.bsky.social use proteomic & phosphoproteomic changes during sexual development to show that TORC1 is reactivated by pheromone signaling @plosbiology.org plos.io/4h3OUVO

How genes and proteins interact with social activities and loneliness for health outcomes
—Proteins associated with social isolation or loneliness and 5 diseases (left below) w/ increased risk
—Genes associated with social activities (right below) w/ protection

Mitochondria and cell death - Nature Cell Biology Several processes of regulated cell death engage or use mitochondria, which are thus central hubs that not only coordinate cell death but also elicit non-lethal signalling mediated by mitochondrial ou...

☕This year, in our #CellDeath focus:
Glover, Schreiner, Dewson & Tait reviewed the intersection of #mitochondria and cell death. #pyroptosis #ferroptosis #necroptosis #apoptosis
👉https://rdcu.be/d46gt
www.nature.com/articles/s41...

🧪 Read the Special Issue of Journal of Proteome Research celebrating the essential contributions that women scientists have made, and are making, in the fields of Proteomics and Metabolomics. ow.ly/OcSl50TWOpU

On the evolutionary developmental biology of the cell Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell ‘omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.

"The development of new tools for manipulating genomes frees us from the limited phenotypes that evolution has produced, allowing us to generate new cell phenotypes and explore the boundaries of cellular novelty." So interesting.
www.cell.com/trends/genet...

Spatial transcriptomic clocks reveal cell proximity effects in brain ageing Nature - A spatially resolved single-cell transcriptomics map of the mouse brain at different ages reveals signatures of ageing, rejuvenation and disease, including ageing effects associated with T...

Thrilled to see this paper out!! 🧪

Spatial transcriptomics of brain aging and 'spatial aging clocks' identify cells that have pro-aging or pro-rejuvenating effects on their neighbors!

Huge CONGRATS to Eric Sun and all authors! Fantastic collaboration with @jameszou.bsky.social!

rdcu.be/d33uQ 🧵

We Are the Analyzers - Proteomics Anthem We Are the Analyzers - A Proteomics Anthem by US HUPO.

We’re thrilled to present "We Are the Analyzers" – an anthem for the proteomics community! A huge shoutout to everyone who brought this incredible song to life. Look what proteomics has already shown us 🎶🧪youtu.be/wzmJDNmsWK8 #Proteomics #USHUPO20YRS

Every glycoprotein resolves into a trail of well-separated glycoforms on isoelectric focusing.. Glad to see 2DE is still in use to resolve proteoforms..