The, Matthew;Samaras, Patroklos;Kuster, Bernhard;Wilhelm, Mathias
Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups
Molecular & Cellular Proteomics
2022
21
12
100437

Giansanti, Piero;Samaras, Patroklos;Bian, Yangyang;Meng, Chen;Coluccio, Andrea;Frejno, Martin;Jakubowsky, Hannah;Dobiasch, Sophie;Hazarika, Rashmi R.;Rechenberger, Julia;Calzada-Wack, Julia;Krumm, Johannes;Mueller, Sebastian;Lee, Chien-Yun;Wimberger, Nicole;Lautenbacher, Ludwig;Hassan, Zonera;Chang, Yun-Chien;Falcomatà, Chiara;Bayer, Florian P.;Bärthel, Stefanie;Schmidt, Tobias;Rad, Roland;Combs, Stephanie E.;The, Matthew;Johannes, Frank;Saur, Dieter;de Angelis, Martin Hrabe;Wilhelm, Mathias;Schneider, Günter;Kuster, Bernhard
Mass spectrometry-based draft of the mouse proteome
Nature Methods
2022

Zecha, Jana;Gabriel, Wassim;Spallek, Ria;Chang, Yun-Chien;Mergner, Julia;Wilhelm, Mathias;Bassermann, Florian;Kuster, Bernhard
Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling
Nature Communications
2022
13
1

Palmblad, Magnus;Böcker, Sebastian;Degroeve, Sven;Kohlbacher, Oliver;Käll, Lukas;Noble, William Stafford;Wilhelm, Mathias
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics
Journal of Proteome Research
2022
21
4
1204-1207

Krumm, Johannes;Sekine, Keisuke;Samaras, Patroklos;Brazovskaja, Agnieska;Breunig, Markus;Yasui, Ryota;Kleger, Alexander;Taniguchi, Hideki;Wilhelm, Mathias;Treutlein, Barbara;Camp, J. Gray;Kuster, Bernhard
High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development
Cell Reports
2022
38
13
110604

Ekvall, Markus;Truong, Patrick;Gabriel, Wassim;Wilhelm, Mathias;Käll, Lukas
Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities
Journal of Proteome Research
2022
21
5
1359-1364

Hamood, Firas;Bayer, Florian P.;Wilhelm, Mathias;Kuster, Bernhard;The, Matthew
SIMSI-Transfer: Software-assisted reduction of missing values in phosphoproteomic and proteomic isobaric labeling data using tandem mass spectrum clustering
Molecular & Cellular Proteomics
2022
100238

Lechner, Severin;Malgapo, Martin Ian P.;Grätz, Christian;Steimbach, Raphael R.;Baron, Agnes;Rüther, Patrick;Nadal, Simon;Stumpf, Carmen;Loos, Christina;Ku, Xin;Prokofeva, Polina;Lautenbacher, Ludwig;Heimburg, Tino;Würf, Vivian;Meng, Chen;Wilhelm, Mathias;Sippl, Wolfgang;Kleigrewe, Karin;Pauling, Josch K.;Kramer, Karl;Miller, Aubry K.;Pfaffl, Michael W.;Linder, Maurine E.;Kuster, Bernhard;Médard, Guillaume
Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target
Nature Chemical Biology
2022

Gabriel, Wassim;Giurcoiu, Victor;Lautenbacher, Ludwig;Wilhelm, Mathias
Predicting fragment intensities and retention time of iTRAQ‐ and TMTPro‐labeled peptides with Prosit‐TMT
PROTEOMICS
2022
2100257

Gabriel, Wassim;The, Matthew;Zolg, Daniel P.;Bayer, Florian P.;Shouman, Omar;Lautenbacher, Ludwig;Schnatbaum, Karsten;Zerweck, Johannes;Knaute, Tobias;Delanghe, Bernard;Huhmer, Andreas;Wenschuh, Holger;Reimer, Ulf;Médard, Guillaume;Kuster, Bernhard;Wilhelm, Mathias
Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides
Analytical Chemistry
2022