MALDI Mass Spectrometry for Quantitative Proteomics - Approaches, Scopes and Limitations. - Andreas Tholey (Computational Proteomics, 2005)

Highly accelerated feature detection in proteomics data sets using modern graphics processing units. - Rene Hussong; Barbara Gregorius; Andreas Tholey; Andreas Hildebrandt 001 (Bioinform., 2009)

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching. - Martin Slawski; Rene Hussong; Andreas Tholey; Thomas Jakoby; Barbara Gregorius; Andreas Hildebrandt 001; Matthias Hein 001 (BMC Bioinform., 2012)

Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. - Anna Katharina Hildebrandt; Ernst Althaus; Hans-Peter Lenhof; Chien-Wen Hung; Andreas Tholey; Andreas Hildebrandt 001 (GCB, 2013)

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data. - Hesham ElAbd; Frauke Degenhardt; Tomás Koudelka; Ann-Kristin Kamps; Andreas Tholey; Petra Bacher; Tobias L. Lenz; Andre Franke; Mareike Wendorff (BMC Bioinform., 2021)