diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition F Meier, AD Brunner, M Frank, A Ha, I Bludau, E Voytik, ... Nature methods 17 (12), 1229-1236, 2020 | 429 | 2020 |
Multi-omic measurements of heterogeneity in HeLa cells across laboratories Y Liu, Y Mi, T Mueller, S Kreibich, EG Williams, A Van Drogen, C Borel, ... Nature biotechnology 37 (3), 314-322, 2019 | 299 | 2019 |
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses G Rosenberger, I Bludau, U Schmitt, M Heusel, CL Hunter, Y Liu, ... Nature methods 14 (9), 921-927, 2017 | 211 | 2017 |
Proteomic and interactomic insights into the molecular basis of cell functional diversity I Bludau, R Aebersold Nature Reviews Molecular Cell Biology 21 (6), 327-340, 2020 | 198 | 2020 |
Complex‐centric proteome profiling by SEC‐SWATH‐MS M Heusel, I Bludau, G Rosenberger, R Hafen, M Frank, ... Molecular systems biology 15 (1), e8438, 2019 | 138 | 2019 |
Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology FM Hansen, MC Tanzer, F Brüning, I Bludau, C Stafford, BA Schulman, ... Nature Communications 12 (1), 254, 2021 | 86 | 2021 |
The structural context of posttranslational modifications at a proteome-wide scale I Bludau, S Willems, WF Zeng, MT Strauss, FM Hansen, MC Tanzer, ... PLoS biology 20 (5), e3001636, 2022 | 72 | 2022 |
A global screen for assembly state changes of the mitotic proteome by SEC-SWATH-MS M Heusel, M Frank, M Köhler, S Amon, F Frommelt, G Rosenberger, ... Cell systems 10 (2), 133-155. e6, 2020 | 66 | 2020 |
AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics WF Zeng, XX Zhou, S Willems, C Ammar, M Wahle, I Bludau, E Voytik, ... Nature Communications 13 (1), 7238, 2022 | 64 | 2022 |
Systematic detection of functional proteoform groups from bottom-up proteomic datasets I Bludau, M Frank, C Dörig, Y Cai, M Heusel, G Rosenberger, P Picotti, ... Nature communications 12 (1), 3810, 2021 | 58 | 2021 |
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes I Bludau, M Heusel, M Frank, G Rosenberger, R Hafen, ... Nature protocols, 1-47, 2020 | 43 | 2020 |
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data A Fossati, C Li, F Uliana, F Wendt, F Frommelt, P Sykacek, M Heusel, ... Nature methods 18 (5), 520-527, 2021 | 37 | 2021 |
ACEseq–allele specific copy number estimation from whole genome sequencing K Kleinheinz, I Bludau, D Hübschmann, M Heinold, P Kensche, Z Gu, ... BioRXiv, 210807, 2017 | 35 | 2017 |
Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling MC Tanzer, I Bludau, CA Stafford, V Hornung, M Mann Nature communications 12 (1), 6053, 2021 | 34 | 2021 |
Parallel accumulation–serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage F Meier, AD Brunner, M Frank, A Ha, I Bludau, E Voytik, ... BioRxiv, 656207, 2019 | 32 | 2019 |
Integrative proteomics reveals principles of dynamic phosphosignaling networks in human erythropoiesis Ö Karayel, P Xu, I Bludau, S Velan Bhoopalan, Y Yao, FC Ana Rita, ... Molecular systems biology 16 (12), e9813, 2020 | 28 | 2020 |
AlphaPept: a modern and open framework for MS-based proteomics MT Strauss, I Bludau, WF Zeng, E Voytik, C Ammar, JP Schessner, ... Nature Communications 15 (1), 2168, 2024 | 27 | 2024 |
Robust dimethyl‐based multiplex‐DIA doubles single‐cell proteome depth via a reference channel M Thielert, ECM Itang, C Ammar, FA Rosenberger, I Bludau, L Schweizer, ... Molecular Systems Biology 19 (9), e11503, 2023 | 25* | 2023 |
SECAT: quantifying protein complex dynamics across cell states by network-centric analysis of SEC-SWATH-MS profiles G Rosenberger, M Heusel, I Bludau, BC Collins, C Martelli, EG Williams, ... Cell systems 11 (6), 589-607. e8, 2020 | 24 | 2020 |
Toward an integrated machine learning model of a proteomics experiment BA Neely, V Dorfer, L Martens, I Bludau, R Bouwmeester, S Degroeve, ... Journal of proteome research 22 (3), 681-696, 2023 | 20 | 2023 |