Froehlich, John W.;Dodds, Eric D.;Wilhelm, Mathias;Serang, Oliver;Steen, Judith A.;Lee, Richard S.
A Classifier Based on Accurate Mass Measurements to Aid Large Scale, Unbiased Glycoproteomics
Molecular & Cellular Proteomics
2013
12
4
1017-1025

Savitski, Mikhail M.;Wilhelm, Mathias;Hahne, Hannes;Kuster, Bernhard;Bantscheff, Marcus
A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets
Molecular & Cellular Proteomics
2015
14
9
2394-2404

Wang, Dongxue;Eraslan, Basak;Wieland, Thomas;Hallström, Björn;Hopf, Thomas;Zolg, Daniel Paul;Zecha, Jana;Asplund, Anna;Li, Li‐hua;Meng, Chen;Frejno, Martin;Schmidt, Tobias;Schnatbaum, Karsten;Wilhelm, Mathias;Ponten, Frederik;Uhlen, Mathias;Gagneur, Julien;Hahne, Hannes;Kuster, Bernhard
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Molecular Systems Biology
2019
15
2

Dai, Chengxin;Füllgrabe, Anja;Pfeuffer, Julianus;Solovyeva, Elizaveta M.;Deng, Jingwen;Moreno, Pablo;Kamatchinathan, Selvakumar;Kundu, Deepti Jaiswal;George, Nancy;Fexova, Silvie;Grüning, Björn;Föll, Melanie Christine;Griss, Johannes;Vaudel, Marc;Audain, Enrique;Locard-Paulet, Marie;Turewicz, Michael;Eisenacher, Martin;Uszkoreit, Julian;Van Den Bossche, Tim;Schwämmle, Veit;Webel, Henry;Schulze, Stefan;Bouyssié, David;Jayaram, Savita;Duggineni, Vinay Kumar;Samaras, Patroklos;Wilhelm, Mathias;Choi, Meena;Wang, Mingxun;Kohlbacher, Oliver;Brazma, Alvis;Papatheodorou, Irene;Bandeira, Nuno;Deutsch, Eric W.;Vizcaíno, Juan Antonio;Bai, Mingze;Sachsenberg, Timo;Levitsky, Lev I.;Perez-Riverol, Yasset
A proteomics sample metadata representation for multiomics integration and big data analysis
Nature Communications
2021
12
1

The, Matthew;Picciani, Mario;Jensen, Cecilia;Gabriel, Wassim;Kuster, Bernhard;Wilhelm, Mathias
AI-Assisted Processing Pipeline to Boost Protein Isoform Detection
Methods in Molecular Biology
Springer US
2024

Chiva, Cristina;Elhamraoui, Zahra;Solé, Amanda;Serret, Marc;Wilhelm, Mathias;Sabidó, Eduard
Assessment and Prediction of Human Proteotypic Peptide Stability for Proteomics Quantification
Analytical Chemistry
2023
95
37
13746-13749

Hoffmann, Nils;Wilhelm, Mathias;Doebbe, Anja;Niehaus, Karsten;Stoye, Jens
BiPACE 2D—graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry
Bioinformatics
2013
30
7
988-995

Zolg, Daniel P;Wilhelm, Mathias;Schnatbaum, Karsten;Zerweck, Johannes;Knaute, Tobias;Delanghe, Bernard;Bailey, Derek J;Gessulat, Siegfried;Ehrlich, Hans-Christian;Weininger, Maximilian;Yu, Peng;Schlegl, Judith;Kramer, Karl;Schmidt, Tobias;Kusebauch, Ulrike;Deutsch, Eric W;Aebersold, Ruedi;Moritz, Robert L;Wenschuh, Holger;Moehring, Thomas;Aiche, Stephan;Huhmer, Andreas;Reimer, Ulf;Kuster, Bernhard
Building ProteomeTools based on a complete synthetic human proteome
Nature Methods
2017
14
3
259-262

Rechenberger, Julia;Samaras, Patroklos;Jarzab, Anna;Behr, Juergen;Frejno, Martin;Djukovic, Ana;Sanz, Jaime;González-Barberá, Eva M.;Salavert, Miguel;López-Hontangas, Jose Luis;Xavier, Karina B.;Debrauwer, Laurent;Rolain, Jean-Marc;Sanz, Miguel;Garcia-Garcera, Marc;Wilhelm, Mathias;Ubeda, Carles;Kuster, Bernhard
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae
Proteomes
2019
7
1
2

Heinzlmeir, Stephanie;Kudlinzki, Denis;Sreeramulu, Sridhar;Klaeger, Susan;Gande, Santosh Lakshmi;Linhard, Verena;Wilhelm, Mathias;Qiao, Huichao;Helm, Dominic;Ruprecht, Benjamin;Saxena, Krishna;Médard, Guillaume;Schwalbe, Harald;Kuster, Bernhard
Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs
ACS Chemical Biology
2016
11
12
3400-3411