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Data-independent acquisition (DIA) proteomics increasingly becomes the method of choice for researchers since it provides better reproducibility, identification rates, and accuracy compared to data-dependent acquisition (DDA). More and more tools are developed for DIA analysis and even established proteomics data processing software now can analyze DIA data. However, analysis of multiplexed spectra, characteristic of DIA, […]

Life as we know it has been shaped by the constraints of the environment. The aerodynamic shape of leaves to prevent the tree from toppling at high winds, or gravity that affects heights of organisms (extraterrestrial humanoids on the fictional pandora in Avatar), or the color of a polar bear. The environment is a critical […]

In the last Journal club, we present a paper by Yilmaz et al. called «De novo mass spectrometry peptide sequencing with a transformer model» [1] introducing a deep learning model for de novo peptide sequencing. What? You do not know exactly what is de novo peptide sequencing? Let me explain it. Imagine that you do […]

In our last Journal Club blog post, we presented ProteomicsML a web platform with tutorials for machine learning in the field of proteomics. Today, we stay on the spot with machine learning, however, on this occasion, we are presenting a new approach and model from Tom Altenburg et al. based on their article “Ad hoc learning […]

Consortium meeting: After we ESRs had participated in the 13th International MaxQuant Summer School on Computational Mass Spectrometry-based Proteomics, the opening dinner of the consortium meeting was the first time that all PROTrEIN members, incl. supervisors, actually met in person. The venue was amazingly beautiful and close to the sea. Where we all enjoyed a […]

Most of us do research because we enjoy finding answers, solving problems and even helping people. But there is also a deep seated human tendency to leave a mark. Contribute to a bigger picture, graffiti on your neighbor’s wall, advance a field. This is probably why we write research papers. (Apart from begging for funding […]

Starting with the premise that I have never organised such a big event in the past, getting actively involved in the organisation of the MaxQuant summer school (MQSS) has been a great opportunity to learn skills that are usually not directly related to pure research in science. The whole process of organising the summer school […]