Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. - Nils Hoffmann; Matthias Keck; Heiko Neuweger; Mathias Wilhelm 001; Petra Högy; Karsten Niehaus; Jens Stoye (BMC Bioinform., 2012)

BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. - Nils Hoffmann; Mathias Wilhelm 001; Anja Doebbe; Karsten Niehaus; Jens Stoye (Bioinform., 2014)

Wilhelm et al. reply. - Mathias Wilhelm 001; Hannes Hahne; Mikhail M. Savitski; Harald Marx; Simone Lemeer; Marcus Bantscheff; Bernhard Küster (Nat., 2017)

ProteomicsDB. - Tobias Schmidt 003; Patroklos Samaras; Martin Frejno; Siegfried Gessulat; Maximilian Barnert; Harald Kienegger; Helmut Krcmar; Judith Schlegl; Hans-Christian Ehrlich; Stephan Aiche; Bernhard Küster; Mathias Wilhelm 001 (Nucleic Acids Res., 2018)

ProteomicsDB: a multi-omics and multi-organism resource for life science research. - Patroklos Samaras; Tobias Schmidt 003; Martin Frejno; Siegfried Gessulat; Maria Reinecke; Anna Jarzab; Jana Zecha; Julia Mergner; Piero Giansanti; Hans-Christian Ehrlich; Stephan Aiche; Johannes Rank; et al. (Nucleic Acids Res., 2020)

PROSPECT: Labeled Tandem Mass Spectrometry Dataset for Machine Learning in Proteomics. - Omar Shouman; Wassim Gabriel; Victor-George Giurcoiu; Vitor Sternlicht; Mathias Wilhelm 001 (NeurIPS, 2022)

ProteomicsDB: toward a FAIR open-source resource for life-science research. - Ludwig Lautenbacher; Patroklos Samaras; Julian Müller 007; Andreas Grafberger; Marwin Shraideh; Johannes Rank; Simon T. Fuchs; Tobias K. Schmidt; Matthew The; Christian Dallago; Holger Wittges; Burkhard Rost; et al. (Nucleic Acids Res., 2022)

PROSPECT PTMs: Rich Labeled Tandem Mass Spectrometry Dataset of Modified Peptides for Machine Learning in Proteomics. - Wassim Gabriel; Omar Shouman; Eva Ayla Schröder; Florian Bößl; Mathias Wilhelm 001 (NeurIPS, 2024)