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: 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
4: 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
5: 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
6: 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
7: Staphylococcal protein A inhibits complement activation by interfering with IgG hexamer formation, Cruz, AR, den Boer, MA, Strasser, J, et al.,
8: 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.
9: 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)
10: 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
11: 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
12: 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
13: 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
14: 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
15: 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
16: 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
17: 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
18: 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
19: 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
20: 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
21: Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16, Pedersen AK, Pfeiffer A, Karemore G, Akimov V, Bekker-Jensen DB, Blagoev B, Francavilla C, Olsen JV., iScience. 2021 Mar 17;24(4):102321. https://doi.org/10.1016/j.isci.2021.102321.
22: Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures. Franciosa G, Smits JGA, Minuzzo S, Martinez-Val A, Indraccolo S, Olsen JV, Nat Commun. 2021 May 4;12(1):2507. https://doi.org/10.1038/s41467-021-22787-9
23: Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users. Chiva C, Mendes Maia T, Panse C. et al., EMBO Rep. 2021 Jun 4;22(6):e52626. https://doi.org/10.15252/embr.202152626. Epub 2021 May 19.
24: Phosphorylation-Dependent Interactome of Ryanodine Receptor Type 2 in the Heart. Chiang DY, Lahiri S, Wang G, et al., Proteomes. 2021 Jun 7;9(2):27. https://doi.org/10.3390/proteomes9020027
25: Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. Schmidt T, Samaras P, Dorfer V, et al., J Proteome Res. 2021 Jun 4;20(6):3388-3394. https://doi.org/10.1021/acs.jproteome.1c00096. Epub 2021 May 10.
26: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Wilhelm M, Zolg DP, Graber M, et al., Nat Commun. 2021 Jun 7;12(1):3346. https://doi.org/10.1038/s41467-021-23713-9. Erratum in: Nat Commun. 2021 Jun 23;12(1):4002.
27: MS Amanda 2.0: Advancements in the standalone implementation. Dorfer V, Strobl M, Winkler S, Mechtler K., Rapid Commun Mass Spectrom. 2021 Jun 15;35(11):e9088. https://doi.org/10.1002/rcm.9088.
28: DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network. Hammond CM, Bao H, Hendriks IA, et al., Mol Cell. 2021 Jun 17;81(12):2533-2548.e9. https://doi.org/10.1016/j.molcel.2021.03.041. Epub 2021 Apr 14.
29: Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. Van Puyvelde B, Van Uytfanghe K, Tytgat O, et al., JACS Au. 2021 Jun 28;1(6):750-765. https://doi.org/10.1021/jacsau.1c00048. Epub 2021 May 3.
30: Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. Taschner M, Basquin J, Steigenberger B, et al., EMBO J. 2021 Aug 2;40(15):e107807. https://doi.org/10.15252/embj.2021107807. Epub 2021 Jun 30.
31: Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Kamel W, Noerenberg M, Cerikan B, et al., Mol Cell. 2021 Jul 1;81(13):2851-2867.e7. https://doi.org/10.1016/j.molcel.2021.05.023. Epub 2021 May 24
32: Similarities and differences in the structures and proteoform profiles of the complement proteins C6 and C7. Lukassen MV, Franc V, Hevler JF, Heck AJR. Proteomics. 2021 Jul 9:e2000310. https://doi.org/10.1002/pmic.202000310. Epub ahead of print.
33: Notch-Jagged signaling complex defined by an interaction mosaic. Zeronian MR, Klykov O, Portell I de Montserrat J, Konijnenberg MJ, Gaur A, Scheltema RA, Janssen BJC. Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2102502118. https://doi.org/10.1073/pnas.2102502118.
34: Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Noberini R, Savoia EO, Brandini S, et al., Clin Epigenetics. 2021 Jul 28;13(1):145. https://doi.org/10.1186/s13148-021-01120-7.
35: Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Mulvey, C.M., Breckels, L.M., Crook, O.M. et al., Nat Commun 12, 5773 (2021). https://doi.org/10.1038/s41467-021-26000-9
36: Neutrophil azurophilic granule glycoproteins are distinctively decorated by atypical pauci- and phosphomannose glycans, Reiding, K.R., Lin, YH., van Alphen, F.P.J. et al., Commun Biol 4, 1012 (2021). https://doi.org/10.1038/s42003-021-02555-7
37: Use of Linear Ion Traps in Data-Independent Acquisition Methods Benefits Low-Input Proteomics, Borràs E, Pastor O, Sabidó E. Anal Chem. 2021 Aug 31;93(34):11649-11653. doi: 10.1021/acs.analchem.1c01885. Epub 2021 Aug 17. PMID: 34404205.
38: Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chains, Hevler JF, Zenezeni Chiozzi R, Cabrera-Orefice A, Brandt U, Arnold S, Heck AJR. Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2106950118. doi: 10.1073/pnas.2106950118.
39: Systems approach reveals distinct and shared signaling networks of the four PGE(2) receptors in T cells, Lone AM, Giansanti P, Jørgensen MJ, et al., Sci Signal. 2021 Oct 5;14(703):eabc8579. doi: 10.1126/scisignal.abc8579. Epub 2021 Oct 5.
40: Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage, Liaci AM, Steigenberger B, Telles de Souza PC, et al.,Mol Cell. 2021 Oct 7;81(19):3934-3948.e11. doi: 10.1016/j.molcel.2021.07.031. Epub 2021 Aug 12. PMID: 34388369.
41: The regulatory landscape of the human HPF1-and ARH3-dependent ADP-ribosylome, Hendriks, I.A., Buch-Larsen, S.C., Prokhorova, E. et al., Nat Commun 12, 5893 (2021). https://doi.org/10.1038/s41467-021-26172-4
42: Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics, Verbruggen S, Gessulat S, Gabriels R, et al.,Mol Cell Proteomics. 2021 Apr 3;20:100076. doi: 10.1016/j.mcpro.2021.100076. Epub ahead of print. PMID: 33823297; PMCID: PMC8214147.
43: Quantifying Positional Isomers (QPI) by Top-Down Mass Spectrometry, Brunner AM, Lössl P, Geurink PP et al.,Mol Cell Proteomics. 2021 Mar 10;20:100070. doi: 10.1016/j.mcpro.2021.100070. Epub ahead of print. PMID: 33711480; PMCID: PMC8099777.
44: DeepLC can predict retention times for peptides that carry as-yet unseen modifications, Bouwmeester, R., Gabriels, R., Hulstaert, N. et al.,Mol Cell Proteomics. 2021 Mar 10; 20:100070. doi: 10.1016/j.mcpro.2021.100070. Epub ahead of print. PMID: 33711480; PMCID: PMC8099777.
45: AKIRIN2 controls the nuclear import of proteasomes in vertebrates, de Almeida, M., Hinterndorfer, M., Brunner, H. et al., Nature 599, 491–496 (2021). https://doi.org/10.1038/s41586-021-04035-8
46: Post-lymphadenectomy Analysis of Exosomes from Lymphatic Exudate/Exudative Seroma of Melanoma Patients, Garcia-Silva S, Ximénez Embún P, Muñoz J, Peinado H., Melanoma, 12 March 2021 Part of the Methods in Molecular Biology book series (MIMB, volume 2265), https://link.springer.com/protocol/10.1007%2F978-1-0716-1205-7_25
47: Molecular characterization of triple negative breast cancer formaldehyde-fixed paraffin-embedded samples by data-independent acquisition proteomics, García-Adrián S, Trilla-Fuertes L, Gámez-Pozo A, et al., Melanoma, Proteomics. 2021 Oct 8:e2100110. doi: 10.1002/pmic.202100110. Epub ahead of print. PMID: 34624180.
48: Structural basis of soluble membrane attack complex packaging for clearance, Van Den Bossche T, Kunath BJ, Schallert K, et al.,Nat Commun 12, 7305 (2021). https://doi.org/10.1038/s41467-021-27542-8
49: DiagnoTop: A Computational Pipeline for Discriminating Bacterial Pathogens without Database Search, VBorges Lima D, Dupré M, Mariano Santos MD, Carvalho PC, Chamot-Rooke J., J Am Soc Mass Spectrom. 2021 Jun 2;32(6):1295-1299. doi: 10.1021/jasms.1c00014. Epub 2021 Apr 15.
50: TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics, Dhenin J, Borges Lima D, Dupré M, Chamot-Rooke J., Bioinformatics, 2021, btab784, https://doi.org/10.1093/bioinformatics/btab784
51: The Human Proteoform Project: Defining the human proteome, Smith LM, Agar J, Chamot-Rooke J, Danis P, Ge Y, Loo J, Pasa-Tolic L, Tsybin YO, Kelleher N. Science advances, 12 Nov 2021, Vol 7, Iss 46, doi:10.1126/sciadv.abk0734
52: Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution, Martinez-Val, A., Bekker-Jensen, D.B., Steigerwald, S. et al., Science advances, Nat Commun 12, 7113 (2021). https://doi.org/10.1038/s41467-021-27398-y
53: Fast Fluoroalkylation of Proteins Uncovers the Structure and Dynamics of Biological Macromolecules, Fojtík L, Fiala J, Pompach P, Chmelík J, Matoušek V, Beier P, Kukačka Z, Novák P., J. Am. Chem. Soc. 2021, 143, 49, 20670–20679, https://pubs.acs.org/doi/10.1021/jacs.1c07771
54: Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex, Loginov DS, Fiala J, Brechlin P, Kruppa G, Novak P., Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics,Volume 1870, Issue 2, 2022, https://www.sciencedirect.com/science/article/pii/S1570963921001412?via%3Dihub
55: Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule assembly, Cereghetti G, Wilson-Zbinden C, Kissling VM, et al., Nat Cell Biol. 2021 Oct;23(10):1085-1094. doi: 10.1038/s41556-021-00760-4. Epub 2021 Oct 6. Erratum in: Nat Cell Biol. 2021 Oct 26;
56: Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1, Harding, R.J., Deme, J.C., Hevler, J.F. et al., Commun Biol 4, 1374 (2021) https://www.nature.com/articles/s42003-021-02895-4
57: Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML., Nicosia, L., Boffo, F.L., Ceccacci, E. et al., Oncogene (2021). https://doi.org/10.1038/s41388-021-02123-7
58: Goat Milk Exosomes As Natural Nanoparticles for Detecting Inflammatory Processes By Optical Imaging, Ana Santos-Coquillat, María Isabel González, Agustín Clemente-Moragón, et al., Small. 2021 Dec 2;e2105421. doi: 10.1002/smll.202105421. Online ahead of print.
59: Temporal and Site-Specific ADP-Ribosylation Dynamics upon Different Genotoxic Stresses, Sara C. Buch-Larsen, Alexandra K.L.F.S.rebak, Ivo. A. Hendriks and Michael L. Nielsen, Cells 2021, 10(11), 2927; https://doi.org/10.3390/cells10112927
60: PDBe-KB: collaboratively defining the biological context of structural data, PDBe-KB consortium, Nucleic Acids Research, Nov 2021, gkab988, https://doi.org/10.1093/nar/gkab988
61: The PRIDE database resources in 2022: A Hub for mass spectrometry-based proteomics evidences, Perez-Riverol Y, Bai J, Bandla C, et al., Nucleic Acids Research, Nov 2021,gkab1038. doi: 10.1093/nar/gkab1038. Online ahead of print.