🔬 New benchmarking study for the proteomics community!
From variability to consensus: PSM rescoring harmonizes peptide identification across search engines and datasets.
Preprint:
doi.org/10.64898/202...

#TeamMassSpec #Proteomics #MassSpectrometry #OpenScience #Benchmarking

GitHub - EuBIC/EuBIC2027: Organizational repository for the EuBIC-MS Hackathon 2027 Organizational repository for the EuBIC-MS Hackathon 2027 - EuBIC/EuBIC2027

📢 Mark your calendars!
We’re excited to announce the EuBIC-MS 2027 Hackathon!

📍 Gimo, Sweden
📅 31 January – 5 February 2027

💡 Have a hackathon idea?
The call for topic proposals is now open on the EuBIC GitHub repository: github.com/EuBIC/EuBIC2...

We’re looking forward to seeing you there!

Hinsehen mit kritischem Geist, Mut und Widerstand Das war ein deutliches Zeichen gegen rechtsextreme Einschüchterungsversuche. Die Ruhr-Universität steht zusammen und sagt: nicht mit uns!

Viele Menschen, eine Botschaft: Wir verteidigen Vielfalt!

Danke an alle RUB-Mitglieder, die dem kurzfristigem Aufruf gefolgt sind und gemeinsam für die Werte der Universität eingestanden haben. Stark! 🤝

📆 Register your interest to join #BioHackEU25 in person!
All expressions of interest will be reviewed, and accepted attendees will be notified by the end of July.

More information: https://loom.ly/UfwZREk

Big thanks to our three speakers for their great talks: Julian Uszkoreit (@uszkoreitju.bsky.social), Yannic Chen, and Harikrishnan Ramadasan (@harirmds.bsky.social).

Also a big thanks to everyone who attended and participated in the discussion session!

#EuPA2025 @eupaproteomics.bsky.social

Is Mark really cuter as PIA, the mascot from the tool with the same name? ;)
github.com/medbioinf/pia

Looking forward to the #EuBIC-MS session at #EuPA2025!

📢 Project Submissions Open for #BioHackathon Germany 2025!
Join us from December 1-5, 2025, at the Anders Hotel in Walsrode. Submit your project proposal by July 15, 2025. Proposals should focus on #bioinformatics challenges and align with de.NBI & ELIXIR-DE activities.
www.denbi.de/de-nbi-event...

Open-Source and FAIR Research Software for Proteomics Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

Fantastic review with an unusual history, growing out of a passionate blog post by @willfondrie.com (willfondrie.com/2024/10/the-...), resulting from a storm (in our teacup) on X during @hupo-org.bsky.social 2024. Great teamwork, authors! pubs.acs.org/doi/10.1021/...

Looking forward to a week of learning about the (responsible) application of AI in proteomics from many of the leaders in the field: www.lorentzcenter.nl/httpswww.cec...

Research Software Trainer | LUMC Do you have a passion for research software and believe in the power of Open Science to drive advancements in healthcare? As a Research Software Trainer at LUMC, you contribute to expanding training c...

Do you have a passion for research software and believe in the power of Open Science to drive advancements in healthcare? If so, we are looking for you! www.lumc.nl/en/about-lum...

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

Wonderful and productive @eubic-ms.org Developers' Meeting in Neustift, South Tyrol, hacking proteomics and metabolomics software and metadata standards for five days!