CNIC Proteomics Lab

First real end-to-end protocol on Wall-E🤖

Huge thanks to #EyownTechnologies and #Opentrons for the support.

Goodbye manual pipetting😝😂

📣Today our colleague Samuel delivered an amazing seminar at the
@eubic-ms.org
Winter School 📣

He shared his single-cell analyses using a new workflow to study PTMs in DIA through open-search, called PTM-Beacon 💻🔍

Congrats!!

Protein Probability Model for High-Throughput Protein Identification by Mass Spectrometry-Based Proteomics Shotgun proteomics is the method of choice for high-throughput protein identification; however, robust statistical methods are essential to automatize this task while minimizing the number of false id...

Last week, our PI Prof. Jesús Vázquez presented at the PD user meeting a seminar on LPGF, a scoring algorithm for protein identification from their identified peptides.

🚀 LPGF has been incorporated as the default protein probability model in the latest version of PD

📄More information at:

We are very happy to have collaborated with María José Fernández-Gómez and Nerea Méndez-Barbero from Patologia Vascular lab in IIS-FJD

We’re proud to share that her poster was selected as the winner of the poster competition at #CNICPhDay!

Congratulations to the whole team for this achievement! 🎉💡

🎓Big congratulations to our colleague Rafa who defended his PhD thesis last week:

His work culminated in the development of Turbomics, a new tool designed to integrative multi-omics analysis. You can read more about it here:

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

Best of luck on your new chapter ahead!

An integrative workflow for quantitative analysis of post-translational modifications (PTMs) in mass spectrometry-based proteomics.

🔬 Captures multiple PTM layers (trypsin efficiency, zonal changes, PTMs, hypermodifications)

⚡ Advanced artifact control

🐭 Uncovering novel oxidative modifications

Integrative multi-layer workflow for quantitative analysis of post-translational modifications Novel algorithms based on ultratolerant database searching have paved the way for comprehensive analysis of all possible post-translational modifications (PTM) that can be detected by mass spectrometr...

🚨 New preprint from @cnicproteomics (CNIC - National Center of Cardiovascular Research, Madrid, Spain) 🚨

📄 Devesa et al. 2025
doi.org/10.1101/2025.01.20.633864

#Proteomics #PTMs #MassSpectrometry #Bioinformatics #OpenSearch #CNICproteomics #Cardiovasculardeseases

Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure a...

📢Publication Alert🌶️! A new HT compatible method for the study of REDOX biology using mass spec has been published by @anamdv.bsky.social at @cnicproteomics.bsky.social! Using using a modified #PACREDOX protocol, to enable fast & robust proteomics! #MagReSynHydroxyl pubs.acs.org/doi/abs/10.1...

P.S. We are looking for an original name for it. Any suggestions?🧐

We had a great training session with the Opentrons team to guide us through the first steps of integrating the robot into our workflows.
We're looking forward to exploring its full potential in the coming weeks.
📸👇
#Proteomics #CNICproteomics #Cardiovasculardeseases #Opentrons #LabAutomation

This week’s news… say hello to our newest lab mate! 🧪🤖

We’re excited to welcome the Opentrons Flex Robot to the team — a modular liquid-handling robot designed for high-throughput and complex workflows that will help us move towards a more automated lab.

The result? It provided the first detailed map of PTM dynamics in the heart and initial evidence for the accumulation of oxidative PTMs after chemotherapy.

#Proteomics #PTMs #SEBBM2025 #MassSpectrometry #CNICproteomics #Cardiovasculardeseases

She introduced a novel PTM workflow that allows the detection not only of individual PTMs but also of hypermodified regions and hypermodified proteins. Applied to myocardial infarction and anthracycline-induced cardiotoxicity, it reveals biologically relevant PTM patterns previously undetectable.

🎙️ Inmaculada Jorge presented "Application of Cutting-edge Proteomics in Biomedical and Clinical Research" at the 47th SEBBM Congress @sebbm.bsky.social, in a symposium coordinated by María Gómez Serrano and Emilio Camafeita.

Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure and function. Redox proteomics, based on the differential alkylation of cysteine sites followed by mass spectrometry, enables the comprehensive analysis of thiol redox status in cells and tissues. However, these approaches require extensive sample manipulation and are not compatible with data-independent acquisition techniques. Here, we introduce PACREDOX, an innovative strategy based on protein aggregation capture (PAC), and demonstrate its compatibility with library-free DIA. Compared with traditional methods such as FASILOX, PACREDOX reduces preparation time and costs while maintaining thiol and proteome coverage. To enable library-free DIA, we corrected in silico spectral libraries in DIA-NN using experimental retention time data from methylthiolated-Cys peptides. PACREDOX with DIA was benchmarked against FASILOX in a myocardial infarction model, yielding the same biological insights, while enhancing peptide and protein coverage. Our results underscore the potential and efficiency of this methodology for studying oxidative damage. Overall, PACREDOX offers an automatable, high-throughput, and cost-effective strategy for redox proteomics.

Our team at the Cardiovascular Proteomics group (CNIC) developed PACREDOX, a new method that combines global + cysteine-redox proteomic profiling in a fast, robust way.

👉 Published in Analytical Chemistry: pubs.acs.org/doi/full/10....

Contact us if you want to get the protocol 🗒️

📢 New paper out!

Oxidative stress disrupts protein homeostasis and is linked to many diseases. To study this, REDOX proteomics is key—but until now, workflows haven’t been very accessible. 👇

We are pleased to collaborate with researchers, clinicians, and industry partners who share our passion for unraveling the whole proteome.

Stay tuned for updates, publications, and opportunities to engage with our team

#Proteomics #MassSpectrometry #OpenSearch #PTMs #CNICproteomics

Our work focuses on developing high-throughput quantitative approaches that allow us to:

1️⃣ Map the landscape of PTMs in complex biological systems.

2️⃣ Provide insights into the molecular mechanisms underlying cardiovascular diseases.

@cnicproteomics.bsky.social is finally in Bluesky!!

Follow us to learn about our quest to advance proteomics research with a special focus on open search strategies and the study of post-translational modifications (PTMs).