Publications 2021

Publications 2021

1: Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions, Martial Rey, Jonathan Dhenin, Youxin Kong et al., Anal Chem. Feb. 22, (2021) https://doi.org/10.1021/acs.analchem.0c04430

2: Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination, Mathieu Dupré, Magalie Duchateau, Christian Malosse, et al., J. Proteome Res. 2021, 20, 1, 202–211, https://doi.org/10.1021/acs.jproteome.0c00351

3: Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks in Vivo, Manuel Matzinger and Karl Mechtler, J. Proteome Res. 2021, 20, 1, 78–93, https://doi.org/10.1021/acs.jproteome.0c00583

4: Glycoproteoform Profiles of Individual Patients’ Plasma Alpha-1-Antichymotrypsin are Unique and Extensively Remodeled Following a Septic Episode, Tomislav Caval, Yu-Hsien Lin, Meri Varkila, et al., Front. Immunol., 14 January 2021 | https://doi.org/10.3389/fimmu.2020.608466

5: Selective cross-linking of coinciding protein assemblies by in-gel cross-linking mass spectrometry, Johannes F Hevler, Marie V Lukassen, Alfredo Cabrera-Orefice et al., EMBO J (2021)40:e106174 https://doi.org/10.15252/embj.2020106174

6: Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ, Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, et al., Cell, Volume 184, Issue 2, https://doi.org/10.1016/j.cell.2020.12.021

7: Mass spectrometry‐based characterization of histones in clinical samples: applications, progresses, and challenges, Roberta Noberini, Giulia Robusti and Tiziana Bonaldi, FEBS J, 2021, epub ahead of print,, https://doi.org/10.1111/febs.15707 

8: Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition, Cabrera-Quio, LE, Schleiffer, A, Mechtler, K, Pauli A., PLOS Genetics, February 18, 2021, https://doi.org/10.1371/journal.pgen.1009390

9: Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation, Cruz, AR, den Boer, MA, Strasser, J, et al.,

10: Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex, Jakob Schnabl, Juncheng Wang, Ulrich Hohmann et al., Genes and Development (2021). Article published online ahead of print http://www.genesdev.org/cgi/doi/10.1101/gad.347989.120.

11: Complete and cooperative in vitro assembly of computationally designed self-assembling protein nanomaterials, Wargacki, A.J., Wörner, T.P., van de Waterbeemd, M. et al., Nat Commun 12, 883 (2021)

12: Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA, Růžena Filandrová, Karel Vališ, Jiří Černý et al., Structure, Vol 29, Issue 4 (2021) Pgs 345-356.e8

13: MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets, Verschaffelt, P., Van den Bossche, T., Gabriel, W., et al., J. Proteome Res. 2021, 20, 4, 2083–2088

14: BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages and Containers, Bai, JW., Bandla, C., Guo, Jx., et al., J. Proteome Res. 2021, 20, 4, 2056–206. https://doi.org/10.1021/acs.jproteome.0c00904

15: MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin, Hendriks, IA, akimov v., Blagoev B., and Nielsen ML. J. Proteome Res. 2021, 20, 4, 2042–2055. https://doi.org/10.1021/acs.jproteome.0c00892

16: QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories, Olivella, Roger, Chiva, Cristina, Serret, Marc et al.J. Proteome Res. 2021, 20, 4, 2010–2013. https://doi.org/10.1021/acs.jproteome.0c00853

17: Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future, Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno, Molecular & Cellular Proteomics, Volume 20, 2021, https://doi.org/10.1016/j.mcpro.2021.100071

18: Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future, Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P., ACS Omega (2021) 6, 15, 10352–10361, DOI:10.1016/j.mcpro.2021.100071

18: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions, Mori M, Zhang Z, Banaei-Esfahani A, et al., Life Mol Systems Biology (2021)17:e9536 https://doi.org/10.15252/msb.20209536

19: MS Annika: A New Cross-Linking Search Engine, Pirklbauer GJ, Stieger CE, Matzinger M, Winkler S, Mechtler K, Dorfer V., J. Proteome Res. 2021, 20, 5, 2560–2569, 2021 https://doi.org/10.1021/acs.jproteome.0c01000

20: Benefits of Ion Mobility Separation and Parallel Accumulation-Serial Fragmentation Technology on timsTOF Pro for the Needs of Fast Photochemical Oxidation of Protein Analysis, Loginov DS, Fiala J, Chmelik J, Brechlin P, Kruppa G, Novak P., ACS Omega (2021) 6, 15, 10352–10361 https://doi.org/10.1021/acsomega.1c00732

21: Deciphering the signaling network of breast cancer improves drug sensitivity prediction, Marco Tognetti, Attila Gabor, Mi Yang, et al., Cell Systems, Volume 12, Issue 5, 2021 https://doi.org/10.1016/j.cels.2021.04.002

22: Crosstalk between H2A variant-specific modifications impacts vital cell functions, Schmücker A, Lei B, Lorković ZJ, et al., PLoS Genet. 2021 Jun 4;17(6):e1009601. (2021) https://doi.org/10.1371/journal.pgen.1009601

23: Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO, Stejskal K, Op de Beeck J, Dürnberger G, Jacobs P, Mechtler K., Anal. Chem. 2021, 93, 25, 8704–8710, 2021 https://doi.org/10.1021/acs.analchem.1c00990