Publications 2022

1: Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry, den Boer MA, Lai SH, Xue X, et al. Anal. Chem. 2022, 94, 2, 892–900,December 23, 2021, DOI: 10.1021/acs.analchem.1c03656

2: Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics, Anal Chem. Ctortecka C, Stejskal K, Krššáková G, et al., 2022 Feb 8;94(5):2434-2443, DOI:10.1021/acs.analchem.1c04174

3: Comparative Proteome Signatures of Trace Samples by Multiplexed Data-Independent Acquisition, Ctortecka C, Krššáková G, Stejskal K, Penninger JM, Mendjan S, Mechtler K, Stadlmann J. Mol Cell Proteomics. 2022 Jan;21(1):100177, DOI:10.1016/j.mcpro.2021.100177  

4: Automated High-Throughput Method for the Fast, Robust, and Reproducible Enrichment of Newly Synthesized Proteins, Vargas-Diaz D, Altelaar M,, J Proteome Res. 2022 Jan 7;21(1):189-199,

5:Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex, Polák M, Yassaghi G, Kavan D, et al.,Anal Chem. 2022 Feb 22;94(7):3203-3210. 

6: High Resolution Proteomic Analysis of Subcellular Fractionated Boar Spermatozoa Provides Comprehensive Insights Into Perinuclear Theca-Residing Proteins, Zhang M, Chiozzi RZ, Skerrett-Byrne DA et al., Front Cell Dev Biol. 2022 Feb 18;

7: A deeper look at carrier proteome effects for single-cell proteomics, Ye Z, Batth TS, Rüther P, Olsen JV,  Commun Biol. 2022 Feb 22;5(1):150. doi: 10.1038/s42003-022-03095-4

8: Combining CRISPRi and metabolomics for functional annotation of compound libraries, Anglada-Girotto M, Handschin G, Ortmayr K. et al., Nat Chem Biol. 2022 May;18(5):482-491. doi: 10.1038/s41589-022-00970-3

9: In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions, Giacobelli VG, Fujishima K, Lepšík M. et al., Mol Biol Evol. 2022 Mar 2;39(3):msac032. doi: 10.1093/molbev/msac032

10: BRCA1 mutations in high-grade serous ovarian cancer are associated with proteomic changes in DNA repair, splicing, transcription regulation and signaling, Giacobelli VG, Fujishima K, Lepšík M. Sci Rep. 2022 Mar 15;12(1):4445. doi: 10.1038/s41598-022-08461-0.

11:  SPIN enables high throughput species identification of archaeological bone by proteomics, Rüther PL, Husic IM, Bangsgaard P et al., Nat Commun 13, 2458 (2022).

12: Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities, Ekvall M, Truong P, Gabriel W, Wilhelm M, Käll L., J. Proteome Res. 2022, 21, 5, 1359–1364,

13:  Predicting fragment intensities and retention time of iTRAQ- and TMTPro-labeled peptides with Prosit-TMT, Gabriel W, Giurcoiu V, Lautenbacher L, Wilhelm M.,  Proteomics. 2022 May 16:e2100257. doi: 10.1002/pmic.202100257.

14: Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development, Naumann C, Heisters M, Brandt W. et al., Curr Biol. 2022 May 23;32(10):2189-2205.e6.

15: Impact of Modified Atmospheres on Growth and Metabolism of Meat-Spoilage Relevant Photobacterium spp. as Predicted by Comparative Proteomics, Fuertes-Perez S, Abele M, Ludwig C et al.,  Frontiers in Microbiology. 2022 ;13:866629.

16: Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas, Walzer M, García-Seisdedos D, Prakash A et al., Sci Data 9, 335 (2022).

17: Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing, Koenig C, Martinez-Val A, Franciosa G, Olsen JV.  Proteomics. 2022 Jun 17:e2100245. doi: 10.1002/pmic.202100245

18: Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows, Matzinger M, Vasiu A, Madalinski M, et al., Nat Commun. 2022 Jul 8;13(1):3975. doi: 10.1038/s41467-022-31701-w. 

19: Panoramic Perspective on Human Phosphosites,Ramasamy P, Vandermarliere E, Vranken WF, Martens L.,J Proteome Res. 2022 Aug 5;21(8):1894-1915. doi: 10.1021/acs.jproteome.2c00164

20: Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation, Yassaghi G, Kukačka Z, Fiala J. et al.,  Anal Chem. 2022 Jul 19;94(28):9993-10002. doi: 10.1021/acs.analchem.1c05476