Publications by authors named "Sander Willems"

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Enhanced Identifications and Quantification through Retention Time Down-Sampling in Fast-Cycling diagonal-PASEF Methods.
Christopher R Below, Oliver M Bernhardt, Stephanie Kaspar-Schönefeld, Sander Willems, Edoardo Coronado

Mol Cell Proteomics· December 2025

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mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format.
Tim Van Den Bossche, Theodore Alexandrov, Aivett Bilbao, Wout Bittremieux, Federico Ivan Brigante, Sander Willems

J Proteome Res· November 2025

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AlphaDIA enables DIA transfer learning for feature-free proteomics.
Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sander Willems

Nat Biotechnol· October 2025

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An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF).
Patricia Skowronek, Georg Wallmann, Maria Wahle, Sander Willems, Matthias Mann

Nat Protoc· June 2025

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AlphaPept: a modern and open framework for MS-based proteomics.
Maximilian T Strauss, Isabell Bludau, Wen-Feng Zeng, Eugenia Voytik, Constantin Ammar, Sander Willems

Nat Commun· March 2024

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Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes.
Constantin Ammar, Julia Patricia Schessner, Sander Willems, André C Michaelis, Matthias Mann

Mol Cell Proteomics· July 2023

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Ethnic minority GP trainees at risk for underperformance assessments: a quantitative cohort study.
Nathanja Mariëtte van Moppes, Sander Willems, Mana Nasori, Jettie Bont, Reinier Akkermans

BJGP Open· March 2023

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Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition.
Patricia Skowronek, Florian Krohs, Markus Lubeck, Georg Wallmann, Ericka C M Itang, Sander Willems

Mol Cell Proteomics· February 2023

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AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics.
Wen-Feng Zeng, Xie-Xuan Zhou, Sander Willems, Constantin Ammar, Maria Wahle

Nat Commun· November 2022

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Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF.
Patricia Skowronek, Marvin Thielert, Eugenia Voytik, Maria C Tanzer, Fynn M Hansen, Sander Willems

Mol Cell Proteomics· September 2022

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The structural context of posttranslational modifications at a proteome-wide scale.
Isabell Bludau, Sander Willems, Wen-Feng Zeng, Maximilian T Strauss, Fynn M Hansen

PLoS Biol· May 2022

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AlphaTims: Indexing Trapped Ion Mobility Spectrometry-TOF Data for Fast and Easy Accession and Visualization.
Sander Willems, Eugenia Voytik, Patricia Skowronek, Maximilian T Strauss, Matthias Mann

Mol Cell Proteomics· March 2022

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A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics.
Bart Van Puyvelde, Simon Daled, Sander Willems, Ralf Gabriels, Anne Gonzalez de Peredo

Sci Data· March 2022

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AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge.
Eugenia Voytik, Isabell Bludau, Sander Willems, Fynn M Hansen, Andreas-David Brunner

Bioinformatics· January 2022

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A large scale mass spectrometry-based histone screening for assessing epigenetic developmental toxicity.
Sigrid Verhelst, Bart Van Puyvelde, Sander Willems, Simon Daled, Senne Cornelis, Ewoud Willems

Sci Rep· January 2022

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An experimental design to extract more information from MS-based histone studies.
Laura De Clerck, Sander Willems, Simon Daled, Bart Van Puyvelde, Sigrid Verhelst

Mol Omics· December 2021

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Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.
Bart Van Puyvelde, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Sander Willems

JACS Au· June 2021

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Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions.
Simon Daled, Sander Willems, Bart Van Puyvelde, Laura Corveleyn, Sigrid Verhelst

Proteomes· April 2021

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Comprehensive histone epigenetics: A mass spectrometry based screening assay to measure epigenetic toxicity.
Sigrid Verhelst, Laura De Clerck, Sander Willems, Bart Van Puyvelde, Simon Daled

MethodsX· September 2020

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Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries.
Bart Van Puyvelde, Sander Willems, Ralf Gabriels, Simon Daled, Laura De Clerck

Proteomics· February 2020

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hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective.
Laura De Clerck, Sander Willems, Roberta Noberini, Camilla Restellini, Bart Van Puyvelde

J Proteome Res· November 2019

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Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human.
Laura De Clerck, Jasin Taelman, Mina Popovic, Sander Willems, Margot Van der Jeught

Sci Rep· November 2019

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Proceedings of the EuBIC Winter School 2019.
Dominik Kopczynski, Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard-Paulet, Sander Willems

EuPA Open Proteom· March 2019

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Forensic tri-allelic SNP genotyping using nanopore sequencing.
Senne Cornelis, Yannick Gansemans, Ann-Sophie Vander Plaetsen, Jana Weymaere, Sander Willems

Forensic Sci Int Genet· January 2019

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Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency.
Guido van Mierlo, René A M Dirks, Laura De Clerck, Arie B Brinkman, Michelle Huth, Sander Willems

Cell Stem Cell· January 2019

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