Blog

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 […]

Changing the proteomics shell towards the DIA-world

27/03/2023 - Journal Club

Changing the proteomics shell towards the DIA-world

by Pinar Altiner and Shamil Urazbakhtin

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, […]

Are you a morning person? – Chronotypes, Circadian Rhythms, and Questionnaires

22/02/2023 - Journal Club

Are you a morning person? – Chronotypes, Circadian Rhythms, and Questionnaires

by Prajwal DSouza and Carlo De Nart

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 […]

Casanovo, a transformer model to identify De novo mass spectrometry peptide sequencing

10/02/2023 - Journal Club

Casanovo, a transformer model to identify De novo mass spectrometry peptide sequencing

by Zahra Elhamraoui and Mostafa Kalhor

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 […]

Ad Hoc Learning of Fragmentation

10/01/2023 - Journal Club

Ad Hoc Learning of Fragmentation

by Zoltan Udvardy and Arslan Siraj

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 […]

Recalling memories of our first in-person project meeting and SciComm training school in the beautiful city of colours ‘Barcelona’

12/12/2022 - News

Recalling memories of our first in-person project meeting and SciComm training school in the beautiful city of colours ‘Barcelona’

by Ayesha Feroz and Alireza Nameni

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 […]

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