Categoría: News

There are enormous amounts of biological cascades in every cell – the smallest functional compartment of our body [1]. Understanding the mechanisms underlying the vast array of phenomena is not only the key element to finding any clues about fatal diseases such as Alzheimer’s and cancer but also to progress in developing treatment for such […]

In our previous Journal Club blog post, we discussed «nanopore profiling,» a method for identifying proteins within the field of proteomics. Today we proceed with «how to validate the identification statistically other than the traditional target-decoy method with an improved version of the decoy-free approach» based on Dominik et al.’s article «Modeling lower-order statistics to […]

Proteins, the mighty microscopic marvels present in what we eat, hence, what we are. In milkshakes 🥤, ice creams 🍦… your hair, your skin… you 👤. These molecular machines are present in all living things, from viruses to the dog 🐶 that barked at you the other day. They are so essential that they keep […]

Hello and welcome back to another issue of the PROTrEIN Journal Club! This occasion we will cover important topics in proteomics, missing values and imputation. We will try to shed light to some of the challenges regarding these matters with the aid of the article titled: “Mass spectrometry-based proteomics imputation using self supervised deep learning” […]

Proteomics research relies heavily on mass spectrometry, which has emerged as the most prominent and widely utilized approach for the identification of proteins. However, progress is being made in other analytical methods for peptides and proteins. In this month PROTrEIN ITN’s Journal Club, we are taking a glance at the characterization of proteins with nanopores […]

The fields of science and technology have been the engines of progress for many years, driving innovation and shaping the world we live in. Contributing to this scientific knowledge and progress is one of the main aspirations most of us researchers have. However, there is a growing number of studies suggesting that scientific progress is […]

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 […]

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 […]

It has been a while since our official PROTrEIN launch. We’ve had monthly ESR meetings during this time, where the majority of us have been able to discuss more details about our projects and present them to the group. Several ESRs are working on developing new tools and data analysis pipelines to improve cross linking […]

The first PROTrEIN annual meeting and summer school took place between the 10th and 23rd of September 2021. Here our ESRs Marc and Mostafa share their thoughts and memories about it.

In this Journal Club, our ESRs Louise and Shamil present the article «Strategies to enable large-scale proteomics for reproducible research» by R. Poulos et al. from July 2020