Ben Orsburn and Ben Neely co-host a podcast series in a “fireside chat” format with prestigious proteomics researchers. The guests are great, the hosts are questionable.

Development release of version 2.0.0 for public testing Code is fully migrated to .NET 8, thus, Mono dependency is obsolete Added an action for automatic building and testing on all code changes A...

You will contribute to the development of core database applications, web services, data ingestion workflows, and the PRIDE Web platform as part of the PRIDE ecosystem. Working closely with the team, ...

An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.

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.

What's Changed small changes in the manuscript by @ypriverol in #65 JOSS citation added. by @ypriverol in #66 ProteomeXchange support by @ypriverol in #67 add to README by @ypriverol in #68 Full...

What's Changed fix bugs and add plots for mzid by @yueqixuan in #295 Multiple fix in mzidentml by @ypriverol in #296 MaxQuant: Fix NaN intensity errors by @cbielow in #304 Fix bug in proteobench_u...

The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...

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Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular me...