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List of works by Mathias Wilhelm

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

scientific article

A classifier based on accurate mass measurements to aid large scale, unbiased glycoproteomics

scientific article published on 25 February 2013

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

scientific article published on 18 February 2019

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

A proteomics sample metadata representation for multiomics integration and big data analysis

scientific article published in 2021

BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry

scientific article published on 20 December 2013

Building ProteomeTools based on a complete synthetic human proteome

scientific article

Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae

scientific article published on 08 January 2019

Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs

scientific article published on 21 October 2016

Chemoproteomic Selectivity Profiling of PIKK and PI3K Kinase Inhibitors

scientific article published on 03 April 2019

Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors

scientific article

CiRCus: A Framework to Enable Classification of Complex High-Throughput Experiments

scientific article published on 22 March 2019

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

scientific article

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

scientific article published on 16 March 2023

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

scientific article published on 07 June 2021

Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics

article published in 2016

Expanding the use of spectral libraries in proteomics

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

scientific article published in 2024

Generating high quality libraries for DIA MS with empirically corrected peptide predictions

scientific article published on 25 March 2020

Global proteome analysis of the NCI-60 cell line panel

scientific article published on 8 August 2013

Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics

scientific article published on 8 August 2014

Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling

scientific article published on 10 January 2022

Mass-spectrometry-based draft of the Arabidopsis proteome

scientific article published on 11 March 2020

Mass-spectrometry-based draft of the human proteome

scientific article (publication date: 29 May 2014)

Meltome atlas-thermal proteome stability across the tree of life

scientific article published on 13 April 2020

Mining the human tissue proteome for protein citrullination

scientific article published on 2 April 2018

Optimized chemical proteomics assay for kinase inhibitor profiling.

scientific article

PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration

scientific article published on 5 September 2017

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms

scientific article published on 30 April 2019

Peptide level turnover measurements enable the study of proteoform dynamics

scientific article published on 2 February 2018

Pharmacoproteomic characterisation of human colon and rectal cancer.

scientific article published on 3 November 2017

Phosphoproteome Profiling Reveals Molecular Mechanisms of Growth-Factor-Mediated Kinase Inhibitor Resistance in EGFR-Overexpressing Cancer Cells

scientific article published on 30 October 2016

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

scientific article published on 27 May 2019

Proteome activity landscapes of tumor cell lines determine drug responses

scientific article published on 20 July 2020

ProteomeTools: Systematic Characterization of 21 Post-translational Protein Modifications by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Using Synthetic Peptides

ProteomicsDB.

scientific article published on 2 November 2017

ProteomicsDB: a multi-omics and multi-organism resource for life science research

scientific article published on 01 January 2020

ProteomicsDB: toward a FAIR open-source resource for life-science research

scientific article published in 2021

Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins

scientific article

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics

scientific article published on 03 April 2021

The target landscape of clinical kinase drugs

scientific article

Trimodal Mixed Mode Chromatography That Enables Efficient Offline Two-Dimensional Peptide Fractionation for Proteome Analysis

scientific article published in August 2017

Wilhelm et al. reply

scientific article published on 01 July 2017

mz5: space- and time-efficient storage of mass spectrometry data sets

scientific article (publication date: 2012)

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