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Cross-Border Collaboration: Enhancing Peptide Identification with MS2Rescore and MS Amanda

08/05/2024 - Journal Club

Cross-Border Collaboration: Enhancing Peptide Identification with MS2Rescore and MS Amanda

by Louise Marie Buur

Back in June of 2022 I left Austria to go on my first secondment in Ghent, Belgium to visit Alireza and the rest of the Compomics group. Besides getting to know the people,  enjoying the summer in the beautiful city and eating numerous waffles, I also did a small project together with members of the […]

Exploring Cellular Complexity: Unveiling Single-Cell Proteomics

08/09/2023 - Journal Club

Exploring Cellular Complexity: Unveiling Single-Cell Proteomics

by Pinar Altiner and Mostafa Kalhor

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 […]

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

23/08/2023 - Journal Club

Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics

by Louise Buur and Arslan Siraj

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 […]

Peptide De Novo Sequencing  What are the ingredients of that delicious pizza?

08/08/2023 - Journal Club

Peptide De Novo Sequencing What are the ingredients of that delicious pizza?

by Prajwal D'Souza and Aditi Sharma

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 […]

Mass spectrometry-based proteomics imputation using self-supervised deep learning

03/08/2023 - Journal Club

Mass spectrometry-based proteomics imputation using self-supervised deep learning

by Zoltan Udvardy and Alireza Nameni

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” […]

Nanopore profiling: a scalable approach to protein identification

22/05/2023 - Journal Club

Nanopore profiling: a scalable approach to protein identification

by Chiara Sopegno and Arthur Grimaud

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 […]

Papers and patents are becoming less disruptive over time

03/04/2023 - Journal Club

Papers and patents are becoming less disruptive over time

by Marc Pauper and Ayesha Feroz

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 […]

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