Esaú Bojórquez Velázquez

Applications are now open for @olgavitek.bsky.social 's May Intitute on computation and statistics for mass spectrometry and proteomics at @northeasternu.bsky.social !

--> computationalproteomics.khoury.northeastern.edu

Dear network. It's a pleasure to share that the Mexican Proteomics Society is organising the tenth edition of our symposium. All omics sciences and systems biology-related topics are welcome! We will share more details soon.

An extraordinary work for the study of molecular markers related to obesity through a proteomic approach. Many thanks to José Ángel Huerta Ocampo and Jaime Delgadillo Velázquez for inviting me to participate in this project.
doi.org/10.1016/j.jp...
#Proteomics
#ExtracellularVesicles
#Obesity

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry
www.nature.com/articles/s41...

YPIC's third event at #EuPA2025 is all about careers. A great opportunity to hear from inspiring professionals and explore your next steps in proteomics. Don't miss it!
#EuPAFPS2025

Unifying the analysis of bottom-up proteomics data with CHIMERYS www.nature.com/artic...

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#proteomics #prot-paper

Novel model organisms and proteomics for a better biological understanding The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full ra…

Model organisms shaped biology—but are they enough? With multi-omics & comparative proteomics, research is moving beyond E. coli & yeast to holobionts & biodiversity.

New commentary out by Jean Armengaud et al.:
www.sciencedirect.com/science/arti...

#Proteomics #Holobiont #Microbiology

Defining Spectral Quality in Mass Spectrometry‐Based Proteomics: A Retrospective Review Mass spectrometry-based proteomics is essential for advancing preventive and personalised medicine. Technological advancements have greatly increased both the number and sensitivity of spectra genera...

Defining Spectral Quality in Mass Spectrometry-Based Proteomics: A Retrospective Review #MassSpectromRev analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10....

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments www.nature.com/artic...

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#proteomics #prot-paper

QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organism Genomes www.biorxiv.org/cont...

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#proteomics #prot-preprint

PCA-N -36,000 human plasma proteomics samples by mass spec in 311 days! WHOOOOOOOOOOOOOOOOOOOOOOOOOOOOOAAAAAAAA!!!!! Dataset for reanalysis alert!!  Mann lab optimized perchlorate based enrichment to get a supe...

36,000 plasma proteomes by mass spectrometry? No nanoparticles?!?! 2,000 protein depth? Can NOT wait to read this. proteomicsnews.blogspot.com/2025/03/pca-...

My @acs.org Priestley award address can be found here
fhalab.caltech.edu/wp-content/u...

The dawn of the revolution that will allow us to precisely describe how microbiomes function The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and …

The dawn of the revolution that will allow us to precisely describe how microbiomes function

Jean Armengaud

www.sciencedirect.com/science/arti...

Thanks for sharing our work!

Proteomic insights into cell signaling and stress response mechanisms in Chaetoceros muelleri under nitrogen limitation Microalgae are often called “green factories” because they can perform photosynthesis, converting sunlight into biomass and high-value metabolites. Ni…

Proteomic insights into cell signaling and stress response mechanisms in Chaetoceros muelleri under nitrogen limitation #JProteomics #MassSpec www.sciencedirect.com/science/arti...

Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein–protein interac...

If you want a free way to organize, filter, share, QC, and visualize proteomics DDA search results you should check out Limelight. A fantastic tool spearheaded by @mriffle.bsky.social
pubs.acs.org/doi/10.1021/...

The Proteoform Program of Life: Deciphering Evolution at the Protein Level pubs.acs.org/doi/10....

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#proteomics #prot-paper

🧪 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

Scientists, given more time and flexibility, often stumble upon unexpected discoveries—like Alexander Fleming, who saw a mould had killed the bacteria he was growing, paving the way for antibiotics.

Recent study analysed such findings—more of them than you'd expect.
👉 www.nature.com/articles/d41...

‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do.

“The leaders of the Human Genome Project always knew they were just starting a conversation”

The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do

https://go.nature.com/40BeQBh

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within the....

In this recently published viewpoint, we look at the promising technique of de novo sequencing and the application of computational algorithms/software to metaproteomics:
doi.org/10.1002/pmic...

#TeamMassSpec #Proteomics #Metaproteomics #Bioinformatics

Plot of the day. 96 wells of goodness in ~24hrs courtesy of your friendly neighborhood Orbitrap Astral. #Proteomics

During my PhD, I enjoyed working with amaranth seeds, which we compared using first-generation proteomics. As a result of this work, we published three scientific papers that I want to share in this first post.

doi.org/10.1016/j.jc...

doi.org/10.1186/s128...

doi.org/10.3390/plan...