Publications by authors named "Mathias Walzer"

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The PRIDE database at 20 years: 2025 update.
Yasset Perez-Riverol, Chakradhar Bandla, Deepti J Kundu, Selvakumar Kamatchinathan, Jingwen Bai, Mathias Walzer

Nucleic Acids Res· January 2025

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Communicating Mass Spectrometry Quality Information in mzQC with Python, R, and Java.
Chris Bielow, Nils Hoffmann, David Jimenez-Morales, Tim Van Den Bossche, Juan Antonio Vizcaíno, Mathias Walzer

J Am Soc Mass Spectrom· August 2024

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OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.
Julianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Mathias Walzer

Nat Methods· March 2024

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TopDownApp: An open and modular platform for analysis and visualisation of top-down proteomics data.
Mathias Walzer, Kyowon Jeong, David L Tabb, Juan Antonio Vizcaíno

Proteomics· February 2024

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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.
Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones, Pierre-Alain Binz, Henry Lam, Mathias Walzer

J Proteome Res· February 2023

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Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.
Mathias Walzer, David García-Seisdedos, Ananth Prakash, Paul Brack, Peter Crowther

Sci Data· June 2022

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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Mathias Walzer

Nucleic Acids Res· January 2022

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Expression Atlas update: gene and protein expression in multiple species.
Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Mathias Walzer

Nucleic Acids Res· January 2022

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OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.
Eugen Netz, Tjeerd M H Dijkstra, Timo Sachsenberg, Lukas Zimmermann, Mathias Walzer

Mol Cell Proteomics· December 2020

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Review of Issues and Solutions to Data Analysis Reproducibility and Data Quality in Clinical Proteomics.
Mathias Walzer, Juan Antonio Vizcaíno

Methods Mol Biol· October 2020

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ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion.
Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes

J Proteome Res· January 2020

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Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma.
Markus W Löffler, Christopher Mohr, Leon Bichmann, Lena Katharina Freudenmann, Mathias Walzer

Genome Med· April 2019

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The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Mathias Walzer

Nucleic Acids Res· January 2019

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Expanding the Use of Spectral Libraries in Proteomics.
Eric W Deutsch, Yasset Perez-Riverol, Robert J Chalkley, Mathias Wilhelm, Stephen Tate, Mathias Walzer

J Proteome Res· December 2018

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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.
Eric W Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Mathias Walzer

J Proteome Res· December 2017

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OpenMS - A platform for reproducible analysis of mass spectrometry data.
Julianus Pfeuffer, Timo Sachsenberg, Oliver Alka, Mathias Walzer, Alexander Fillbrunn

J Biotechnol· November 2017

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The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics.
Juan Antonio Vizcaíno, Gerhard Mayer, Simon Perkins, Harald Barsnes, Marc Vaudel, Mathias Walzer

Mol Cell Proteomics· July 2017

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A community proposal to integrate proteomics activities in ELIXIR.
Juan Antonio Vizcaíno, Mathias Walzer, Rafael C Jiménez, Wout Bittremieux, David Bouyssié

F1000Res· June 2017

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ImmunoNodes - graphical development of complex immunoinformatics workflows.
Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher

BMC Bioinformatics· May 2017

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The Human Proteome Organization-Proteomics Standards Initiative Quality Control Working Group: Making Quality Control More Accessible for Biological Mass Spectrometry.
Wout Bittremieux, Mathias Walzer, Stefan Tenzer, Weimin Zhu, Reza M Salek

Anal Chem· April 2017

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Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient".
Markus W Löffler, P Anoop Chandran, Karoline Laske, Christopher Schroeder, Irina Bonzheim, Mathias Walzer

J Hepatol· January 2017

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Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient.
Markus W Löffler, P Anoop Chandran, Karoline Laske, Christopher Schroeder, Irina Bonzheim, Mathias Walzer

J Hepatol· October 2016

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Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.
Johannes Griss, Yasset Perez-Riverol, Steve Lewis, David L Tabb, José A Dianes, Mathias W Walzer

Nat Methods· August 2016

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OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
Hannes L Röst, Timo Sachsenberg, Stephan Aiche, Chris Bielow, Hendrik Weisser, Mathias Walzer

Nat Methods· August 2016

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FRED 2: an immunoinformatics framework for Python.
Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr

Bioinformatics· July 2016

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