Edu Chicano

Comparative evaluation of analytical methods for CSF proteomics link.springer.com/ar...

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#proteomics #prot-paper

prepIMS: a Robust Data Preprocessing Workflow for Ion Mobility Mass Spectrometry Imaging Publication date: Available online 28 November 2025 Source: Analytica Chimica Acta Author(s): Linlin Wang, Chengyi Xie, Lei Guo, Thomas Ka Yam Lam, Chris Kong Chu Wong, Mudassir Shah, Xiangnan Xu, Jianing Wang, Jingjing Xu, Jiyang Dong, Zongwei Cai

(ACA) prepIMS: a Robust Data Preprocessing Workflow for Ion Mobility Mass Spectrometry Imaging: Publication date: Available online 28 November 2025

Source: Analytica Chimica Acta

Author(s): Linlin Wang, Chengyi Xie, Lei Guo, Thomas Ka Yam Lam, Chris Kong Chu Wong, Mudassir… #AChimActa #MassSpecRSS

Rapid assay development for low input targeted proteomics using a versatile linear ion trap - Nature Communications Advances in proteomics enable studying limited cell populations, typically requiring high mass accuracy instruments. Here, the authors present a workflow using a unit mass resolution linear ion trap to develop targeted assays from global measurements with free software.

Rapid assay development for low-input targeted proteomics using a linear ion trap — a promising step toward accessible, high-sensitivity proteomics workflows.

🔗 www.nature.com/articles/s41...

Looking to master Skyline but lack time? Skyline Online returns!

Join our accelerated Small Molecule course Oct 8-10, 9am-5pm EST, covering comprehensive Skyline applications in metabolomics, lipidomics, and beyond for MS data from any major vendor.

Just $175 USD to go from intro to expert.

We’re excited to invite you to a career panel discussion featuring three outstanding speakers: Rudolf Aebersold, Marcus Bantschoff, Pascal Gaudet
📅 Date: November 27
⏰ Time: 2:00 PM
Don't miss it out and hear the inspiration from leaders in the field!
👉 Register here: docs.google.com/forms/d/e/1F...

A Compendium of Bona Fide Reference Markers for Genuine Plant Extracellular Vesicles and Their Degree of Phylogenetic Conservation Although the field of plant EVs (PEVs) is experiencing exponential growth, rigorous characterisation complying with MISEV guidelines has not been yet implemented due to the lack of bona fide referenc....

NEW PUBLICATION FROM THE GROUP IN #JEV!
A compendium of bona fide reference markers for plant #EVs🌿
isevjournals.onlinelibrary.wiley.com/doi/10.1002/...
🙌 Impressive work by: Miriam M.R. de Lope, Ibone Rubio, @educhicano.bsky.social and more!
@isev.org @snevresearch.bsky.social
Highlights here!👇

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results FragPipe is recognized as one of the fastest computational platforms in proteomics, making it a practical solution for the rapid quality control of high-throughput sample analyses. Starting with version 23.0, FragPipe introduced the “Generate Summary Report” feature, offering .pdf reports with essential quality control metrics to address the challenge of intuitively assessing large-scale proteomics data. While traditional spreadsheet formats (e.g., tsv files) are accessible, the complexity of the data often limits user-friendly interpretation. To further enhance accessibility, PSManalyst, a Shiny-based R application, was developed to process FragPipe output files (psm.tsv, protein.tsv, and combined_protein.tsv) and provide interactive, code-free data visualization. Users can filter peptide-spectrum matches (PSMs) by quality scores, visualize protease cleavage fingerprints as heatmaps and SeqLogos, and access a range of quality control metrics and representations such as peptide length distributions, ion densities, mass errors, and wordclouds for overrepresented peptides. The tool facilitates seamless switching between PSM and protein data visualization, offering insights into protein abundance discrepancies, samplewise similarity metrics, protein coverage, and contaminants evaluation. PSManalyst leverages several R libraries (lsa, vegan, ggfortify, ggseqlogo, wordcloud2, tidyverse, ggpointdensity, and plotly) and runs on Windows, MacOS, and Linux, requiring only a local R setup and an IDE. The app is available at (https://github.com/41ison/PSManalyst.

It's now properly published. If you want to easily check important characteristics of your data before diving into complicated statistics, check out PSManalyst.

PSManalyst: A Dashboard for Visual Quality Control of FragPipe Results | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

The three horsemen of the apocalypse
… hahahahahaha

Enhancing Lipidomics With High‐Resolution Ion Mobility‐Mass Spectrometry PROTEOMICS, EarlyView.

(Proteomics) Enhancing Lipidomics With High‐Resolution Ion Mobility‐Mass Spectrometry: PROTEOMICS, EarlyView. #MassSpecRSS

This week’s #THEProteomicsShow continues to explore #AltProteomics, but this time more about the data. Ben @proteomicsnews.bsky.social and I sat down with Yasset @ypriverol.bsky.social and talked about non-mass spec data and related aspects. Find it wherever you find fine podcasts and enjoy!

[ASAP] Subcellular-Resolution Molecular Pathology by Laser Ablation–Rapid Evaporative Ionization Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.5c02013

(ACS Anal Chem) [ASAP] Subcellular-Resolution Molecular Pathology by Laser Ablation–Rapid Evaporative Ionization Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.5c02013 #MassSpecRSS #ACSAChem

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Neutrophils are k...

Happy to share our latest preprint doing low cell number (mini-bulk) and single cell #proteomics on tumour associated neutrophils from human glioblastoma where we find multiple functional states that would be invisible to scRNAseq, some showing pro-tumoural states with potential therapeutic value

Watch out timsTOF HT acquire proteomics data in real time!! YouTube video by Brett Phinney

Want to watch our timsTOF HT and Evosep acquire 100 bat plasma samples in real time? I know you do!! Will the column clog or things break? Tune in to find out!! I'm obviously procrastinating btw 😉
www.youtube.com/live/Mb2pJpQ...

We visited the IMIBIC Mass Spectrometry and Molecular Imaging Unit (IMSMI lab) in #Córdoba, headed by @educhicano.bsky.social‬. Edu’s team and the Advanced Microscopy unit (Gema García Jurado and Álvaro Carrasco Carmona) warmly welcomed us and shared their spatial omics knowledge.

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...

SPROUTS_DB: an implemented database of contaminants for extracellular vesicle proteomics studies www.biorxiv.org/cont...

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#proteomics #prot-preprint

In-depth and high-throughput spatial proteomics for whole-tissue slice profiling by deep learning-facilitated sparse sampling strategy www.nature.com/artic...

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#proteomics #prot-paper

Advances in total glycomic analysis including sialylated sub-glycan isomers by SALSA method All eukaryotic cell surfaces are coated with various types of glycans, which are essential molecules in biological events. In this review, we summariz…

Advances in total glycomic analysis including sialylated sub-glycan isomers by SALSA method #BBAAdv #MassSpec www.sciencedirect.com/science/arti...

(BioRxiv All) Proteomic profiling uncovers sexual dimorphism in the muscle response to wheel running exercise in the FLExDUX4 murine model of facioscapulohumeral muscular dystrophy: FLExDUX4 is a murine experimental model of facioscapulohumeral muscular… http://dlvr.it/TJb0SP #BioRxiv #MassSpecRSS

🌟 Life Science Tools (Single-Cell, Spatial Biology, Proteomics, Next-Gen Sequencing)
Strongest growth drivers:
Single-cell and Spatial Omics:

10X Genomics ($TXG), NanoString (part of Bruker $BRKR), Akoya (part of Quanterix $QRTX), and emerging players like Vizgen.

DDM (n-dodecyl β-D-maltoside). This seems too good to be true?! It's giving us a huge boost in hydrophobic peptide signal.

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 ⬇️

Mass calibration algorithm in DIA-NN 2.0 can successfully correct even for the below 🙄😊. Apparently this kind of things can happen to some instruments.

If you spot sth odd in your data - please always let us know, sometimes troubleshooting is really quick and interesting things are discovered.

Courses at EMBL-EBI Data science for life scientists. Hinxton. Closes 2 March. Data visualisation for biology. Hinxton. Closes 9 March. Systems biology: from large datasets to biological insight. Hinxton. Closes 16 March. Proteomics bioinformatics. Hinxton. Closes 6 April.

We have several courses open for applications - whether you're a #lifescientist hoping to get to grips with #datascience, or you want to improve your #dataviz skills or you're hoping to learn about #omics and #bioinformatics then take a look!

More info: ebi.ac.uk/training/liv...

🧪🧬🖥️ #GeneSky

❗The Deadline for our EuPA Awards is extended to 16th of March❗
Send in now your application and join us at the #EuPA-FPS2025. We are looking forward to you EuPA Awards Application!

Hi all, the Finnish Proteomics Society is now on Bluesky! We just elected a new board and are ready to dive into new adventures.

#Finland #Proteomics #MassSpec #education @eupaproteomics.bsky.social

❗Only 3 days left to register ❗Join our 2nd YPIC Annual Proteomics Gathering in Athens. One day with fruitful discussions, amazing presentations, and a lot of networking! Here is the link to register: docs.google.com/forms/d/e/1F...

icbl2025.at
From today, registration for the #icbl2025 is open!
Don't miss this fantastic meeting and a gorgeous venue!

News in Proteomics Research blog post | Immunopeptidomics on low cell numbers without crappy antibodies! proteomicsnews.blogs...

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#proteomics #prot-other

Release DIA-NN 2.0 · vdemichev/DiaNN We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

DIA-NN 2.0 is released! We consider it the biggest step forward in the history of DIA-NN. On modern LC-MS almost all identifications are now peptidoform-confident, with major improvements e.g. for phospho. Some other cool things too: github.com/vdemichev/Di...