
08/09/2023 - Journal Club
Exploring Cellular Complexity: Unveiling Single-Cell Proteomics
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 […]

23/08/2023 - Journal Club
Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics
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 […]

08/08/2023 - Journal Club
Peptide De Novo Sequencing What are the ingredients of that delicious pizza?
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 […]

03/08/2023 - Journal Club
Mass spectrometry-based proteomics imputation using self-supervised deep learning
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” […]

22/05/2023 - Journal Club
Nanopore profiling: a scalable approach to protein identification
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 […]

03/04/2023 - Journal Club
Papers and patents are becoming less disruptive over time
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 […]

27/03/2023 - Journal Club
Changing the proteomics shell towards the DIA-world
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, […]

22/02/2023 - Journal Club
Are you a morning person? – Chronotypes, Circadian Rhythms, and Questionnaires
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 […]

10/02/2023 - Journal Club
Casanovo, a transformer model to identify De novo mass spectrometry peptide sequencing
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 […]

10/01/2023 - Journal Club
Ad Hoc Learning of Fragmentation
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 […]

16/11/2022 - Journal Club
New to machine learning in proteomics? Check out the ‘ProteomicsML’ web platform
Machine learning approaches have become an established part of the mass spectrometry-based proteomics field in recent years. Several tools capable of predicting different aspects of peptide behavior have been developed and incorporated in data analysis workflows. These tools have proven to be beneficial in peptide and protein identification in proteomics experiments, and it is therefore […]

26/06/2022 - Journal Club
“Cross-Linking Mass Spectrometry: A sneak peak into its world!! ”
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 […]

20/05/2022 - Journal Club
A Systematic Review on Bioethics in Proteomics
The moment to begin exercising control over the rules and regulations that will bind us tomorrow is soon. The time to begin thinking and talking about them is now. In this month’s Journal Club, we have decided to step away from technical topics such the latest advances in proteomics methodologies. Instead, we will approach a more “philosophic” […]

15/04/2022 - Journal Club
Adding the third dimension to protein modifications analysis
Short description In the study of post-translational modifications from mass spectrometry experiments, proteins are almost always represented as a linear string of amino acids. However, it should be kept in mind that proteins’ function is conferred by their 3-dimensional structure and that understanding the modifications of proteins calls for studying them in their structural context. […]

28/03/2022 - Journal Club
Machine Learning Algorithms Applications in fMRI Data Analysis
The article Performance of machine learning classification models of autism using resting-state fMRI is contingent on sample heterogeneity (Maya A. Reiter, Afrooz Jahedi, A. R. Jac Fredo, Inna Fishman, Barbara Bailey, Ralph-Axel Müller, Springer Nature 2020) was chosen because it shows potential applications of machine learning in fMRI data analysis. Unsupervised machine learning has been […]