Andrea Petretto

MetaXtract: Extracting Metadata from Raw Files for FAIR Data Practices and Workflow Optimisation www.biorxiv.org/cont...

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#proteomics #prot-preprint

Current efforts focus on predicting transcriptional responses to gene silencing.

Even if spectacularly successful, they leave open key questions:
◾️Functions of genetic mutations & polymorphisms
◾️Proteoform functions
◾️Protein abundance regulation

Biology is complex.

Can we all agree to write all the grants in the first semester so we can do other things during the second semester?

thanks! but for the heat? This, for me, is a huge problem..

This is the typical solution for noise. Otherwise, you can put the pumps behind a wall.
Noise reduction box for your vacuum pump share.google/INWVOMRy4bH9...

We're planning the new labs at my institute. I'd be interested in anyone's suggestions on how to manage noise and heat from the pumps :)

Pretty cool update from GlycoScape:
Sugar-specific visualisation, based on the sugar type. Should help for hypothesis generation since you can plot each sugar type and compare.

Out in @cp-cellsystems.bsky.social‬: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @kimbakjensen.bsky.social. Lead author Frederik Post explains below:

I want to start a new global movement:
Meetless Monday - we encourages people to reduce their meeting activity by one day each week for personal health and the planet's well-being.

News in Proteomics Research blog post | Mass spectrometry proteomics - From single cells through new(!) clinical applications! proteomicsnews.blogs...

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#proteomics #prot-other

Scalable Acid-Aided Lysis of Skin Samples Improves Proteome Coverage www.sciencedirect.co...

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#proteomics #prot-paper

Computational mass spectrometry for exposomics in non‑target screening - Analytical and Bioanalytical Chemistry

(ABioanChem) Computational mass spectrometry for exposomics in non‑target screening #MassSpecRSS

QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets PROTEOMICS, EarlyView.

(Proteomics) QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry‐Based Proteomics Datasets: PROTEOMICS, EarlyView. #MassSpecRSS

His website is equally amazing, especially the haikus

hairyfatguy.com/lutefisk/

📢 Happy to announce that Ensembl 115 and Ensembl Genomes 62 are out! This release features ~120000 new protein coding transcripts in human GRCh38, 2 new cattle, 7 new plants and 20 new metazoa! 🧬🐮 🫛🪲
Read more here ➡️ zurl.co/poyXM

This provocative article does not mince words.

The authors argue that genome sequencing and scRNA-seq yield findings challenging the notion that cancer is a ‘genetic disease’:

"... the cancer research community has abandoned deep thinking for deep sequencing"

1/n

Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples pubs.acs.org/doi/10....

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#proteomics #prot-paper

Nice to see our SUGA approach on PanoramaWeb. It hosts our raw files and Skyline assays, to improve data analysis reproducibility.
Quick and easy N-glycomics, suitable for those trying out glycan analysis without spending extra $ on anything except PNGase-F!
Paper: pubmed.ncbi.nlm.nih.gov/39978775/

How to Apply Learn more about our application process

If you are interested in scientific software engineering or experimental work in the fields of spatial and multi-modal -omics, high throughput interaction proteomics, or mass instrumentation, apply until Oct 7th! @mannlab.bsky.social
www.biochem.mpg.de/mann
imprs-ml.mpg.de/How-to-Apply

Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction - BMC Microbiology Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability w...

Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction #BMCMicrobiol #MassSpec bmcmicrobiol.biomedcentral.com/articles/10....

Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics - Nature Communications Accurate metabolite annotation remains a major challenge in untargeted metabolomics. Here, the authors present MetDNA3, a framework that integrates knowledge and data-driven two-layer networking to improve both the accuracy and coverage of known metabolite annotation, while also enabling the discovery of uncharacterized metabolites.

Knowledge and data-driven two-layer networking for accurate metabolite annotation in untargeted metabolomics #nature #MassSpecRSS

[ASAP] Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00179

(JASMS) [ASAP] Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00179 (RSS) #MassSpecRSS #JASMS

[ASAP] A Chromatography-Guided Co-Fractionation Mass Spectrometry Strategy for Rapid Profiling of Drug-Perturbed Protein Complexes Analytical ChemistryDOI: 10.1021/acs.analchem.5c02702

(ACS Anal Chem) [ASAP] A Chromatography-Guided Co-Fractionation Mass Spectrometry Strategy for Rapid Profiling of Drug-Perturbed Protein Complexes: Analytical ChemistryDOI: 10.1021/acs.analchem.5c02702 #MassSpecRSS #ACSAChem

Integration of cell-type resolved spatial proteomics and transcriptomics reveals novel mechanisms in early ovarian cancer High-grade serous carcinoma (HGSC) is the most common ovarian cancer subtype, typically diagnosed at late stages with poor prognosis. Understanding early molecular events driving HGSC progression is c...

Spatial proteomics & transcriptomics chart #ovariancancer evolution from fallopian tube precursors. Deep Visual Proteomics reveals early SUMOylation, TRIP13 epithelial driver, BGN therapeutic target & epithelial-stromal cooperation in progression.
www.medrxiv.org/content/10.1...

PXD056888 🚨

Metaproteomes of six ex vivo human gut microbiota generating 4.6 million microbial protein responses.

🚨 New dataset alert! 🚨

Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics Field Asymmetric Ion Mobility Spectrometry (FAIMS) enhances signal to noise ratio filtering ions based on their differential mobility, making it an indispensable tool for single-cell and low-input pro...

It is an honor to inform you that our manuscript with low resolution FAIMS is now online

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

Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child Proceedings of the National Academy of Sciences, Volume 122, Issue 34, August 2025. SignificanceWe report an advance in antibody discovery, by identifying naturally acquired broadly inhibitory human monoclonal antibodies againstPlasmodium falciparummalaria parasites directly from plasma using mass spectrometry. This represents a ...

(PNAS) Identification of broadly inhibitory anti-PfEMP1 antibodies by mass spectrometry sequencing of plasma IgG from a malaria-exposed child: Proceedings of the National Academy of Sciences, Volume 122, Issue 34, August 2025.
SignificanceWe report an advance in antibody… #PNAS #MassSpecRSS

Next Generation MasSpec Pen Technology: Innovations in Instrumentation and Medical Device Development for Intraoperative Use Publication date: Available online 26 August 2025 Source: International Journal of Mass Spectrometry Author(s): Charles A. Wolfe, Sydney Povilaitis, Michael F. Keating, Ashley E. Montgomery, Bryan M. Burt, Amir A. Jazaeri, Livia S. Eberlin

(IJMS) Next Generation MasSpec Pen Technology: Innovations in Instrumentation and Medical Device Development for Intraoperative Use: Publication date: Available online 26 August 2025

Source: International Journal of Mass Spectrometry

Author(s): Charles A. Wolfe, Sydney… #ijms #MassSpecRSS

Impressive work from great colleagues at RKI. Ultra-fast virus 🦠 diagnostics with mass spec.

Original publication on vPro-MS here:
www.nature.com/articles/s41...

We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction

🔗
www.biorxiv.org/content/10.1...

📦
saezlab.github.io/MetaProViz/

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