Publications 2020

1: How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by integrative structural mass-spectrometry, Pascal Albanese, Sem Tamara, Guido Saracco, Richard A. Scheltema, Cristina Pagliano, Nat Commun 11, 1361 (2020). https://doi.org/10.1038/s41467-020-15184-1

2. Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context, Ramasamy P, Turan D, Tichshenko N, Hulstaert N, Vandermarliere E, Vranken W, Martens L., Proteome Res.2020,2020, 19, 8, 3478–3486, Publication Date:June 8, 2020 https://doi.org/10.1021/acs.jproteome.0c00306

3. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis, Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, MuthT., https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00136

4. Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times, Bouwmeester R, Martens L, Degroeve S. Chem.2020, 92, 9, 6571–6578, Publication Date:April 13, 2020; https://doi.org/10.1021/acs.analchem.0c00233; 

5: Robust Summarization and Inference in Proteome-wide Label-free Quantification, Adriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement, Molecular & Cellular Proteomics July 1, 2020, April 22, 2020, 19 (7) 1209-1219; do1: 10.1074/mcp.RA119.001624

6: Fishing for newly synthesized proteins with phosphonate-handles, Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Nat Commun. 2020;11(1):3244. Published 2020 Jun 26. doi:10.1038/s41467-020-17010- (https://www.nature.com/articles/s41467-020-17010-0).

7: A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes, Beveridge R, Stadlmann J, Penninger JM, Mechtler K. Nat Commun. 2020;11(1):742. Published 2020 Feb 6. doi:10.1038/s41467-020-14608-2 (https://www.nature.com/articles/s41467-020-14608-2)

8: The age of data driven Proteomics: How machine learning enables Novel Workflows , Bouwmeester, Robbin & Gabriels, Ralf & Van Den Bossche, Tim & Martens, Lennart & Degroeve, Sven. (2020). PROTEOMICS. 10.1002/pmic.201900351 (https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201900351)

9: Generating high quality libraries for DIA MS with empirically corrected peptide predictions, Brian C. Searle, Kristan E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Sigfried Gessulat, Bernhard Küster & Mathias Wilhelm, Nat Commun, 2020 march 5, Volume 11, Article number 1548 (2020) DOI https://doi.org/10.1038/s41467-020-15346-1: https://www.nature.com/articles/s41467-020-15346-1

10:  The omics discovery REST interface, Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A Grüning, Henning Hermjakob, Yasset Perez-Riverol, Nucleic Acids Research, 2020 May 6 pii: gkaa326. doi:10.1093/nar/gkaa326. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa326/5831190

11: ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin(STAG1) from WAPL,  Gordana Wutz, Rene Ladurner, Brian Glen St Hilaire, et al., JM, ELIFE, Volume: 9, Article Number: e52091, Published: FEB 17 2020, https://elifesciences.org/articles/52091

12: FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics, Kyowon Jeong, Jihyung Kim, Manasi Gaikwad, Siti Nurul Hidayah, Laura Heikaus, Hartmut Schluter, Oliver Kohlbacher, CELL SYSTEMS  , Volume: 10   Issue: 2   Pages: 213-+   Published: FEB 26 2020, https://doi.org/10.1016/j.cels.2020.01.003 https://www.sciencedirect.com/science/article/pii/S2405471220300302

13: The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics, Eric W. Deutsch, Nuno Bandeira, Vagisha Sharma, et al., Nucleic Acids Research, Jan 8 2020, Vol. 48, Issue: D1 Pages: D1145-D1152, doi:10.1093/nar/gkz984.

14: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries, Bart Van Puyvelde, Sander Willems, Ralf Gabriels, et al., Proteomics 2020, 20, Feb 2020, Issue 3-4, 1900306, doi:10.1002/pmic.201900306

15: To Cleave or Not To Cleave in XL-MS? Steigenberger, P. Albanese, A. J. R. Heck, and R. A. Scheltema, Journal of the American Society for Mass Spectrometry 2020 31 (2), 196-206, DOI: 10.1021/jasms.9b00085, https://pubs.acs.org/doi/10.1021/jasms.9b00085

16: Resolving heterogeneous macromolecular assembles by Orbitrap-based single-particle charge detection mass spectrometry, Wörner, T.P., Snijder, J., Bennett, A., Mavis Agbandje-McKenna, alexander A Makarov, Albert J R Heck, Nat Methods 17, 395–398 (2020). https://doi.org/10.1038/s41592-020-0770-7

17: Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control, Teresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, Francis Impens, ACS Omega, 2020, 5, 12, 6754-6762, March 17, 2020, https://doi.org/10.1021/acsomega.0c00080

18: N-terminal proteoforms in human disease, Annelies Bogaert, Maria Fernandez and  Kris Gevaert, (2020) Trends in Biochemical Sciences 45(4). 308-320, Published online 27 Jan 2020, https://doi.org/10.1016/j.tibs.2019.12.009

19: A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients, Dorte B. Bekker-Jensen, Ana Martinez-Val, Sophia Steigerwald , et al., Molecular & Cellular Proteomics February 12, 2020, doi: 10.1074/mcp.TIR119.001906

20: Influence of cross-linker polarity on selectivity towards lysine side chains, Jan Fiala, Zdeněk Kukačka, Petr Novák, Journal of Proteomics, Volume 218, 30 April 2020, 103716, https://doi.org/10.1016/j.jprot.2020.103716

21: COSS: A fast and user-friendly tool for spectral library searching, Shiferaw GA, Vandermarliere E, Hulstaert N, Gabriels R, Martens L, Volders PJ, J Proteome Res. 2020 May 8. doi: 10.1021/acs.jproteome.9b00743

22: Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides, Manuel Matzinger, Wolfgang Kandioller, Philipp Doppler, Elke H. Heiss, and Karl Mechtler, Journal of Proteome Research2020 19 (5), 2071-2079, doi: 10.1021/acs.jproteome.0c00003

23: Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries, Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, et al., Nat Commun, 2020 Feb 7;11(1):787. volume 11, Article number: 787 (2020) [PubMed] doi: 10.1038/s41467-020-14609-1.

24: Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling,  Oleg Klykov, Carmen van der Zwaan,  Albert J.R. Heck, Alexander B. Meijer,  Richard A. Scheltema, Proc Natl Acad Sci U.S.A.2020 Jan 28;117(4):1976-1987 , doi: 10.1073/pnas.1911785117. Epub jan 2020 Jan 10[PubMed]

25: EPIFANY – A method for efficient high-confidence protein inference. Julianus Pfeuffer, Timo Sachsenberg, Tjeerd M. H. Dijkstra, Oliver Serang, Knut Reinert, Oliver Kohlbacher, J Proteome Res.2020 Jan 24. doi: 10.1021/acs.jproteome.9b00566

26: Chromatin-Bound Proteome Profiling by Genome Capture, Aranda, S., Borràs, E., Sabidó, E., & Di Croce, L., STAR protocols, 2020, 1 (1) 100014, DOI: 10.1016/j.xpro.2020.100014

27: Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes, Zhu, J; Lin, YH; Dingess, KA; Mank, M; Stahl, B; Heck, AJR , Proteome Research, 2020, 19 (5) 1941-1952, doi:10.1021/acs.jproteome.9b00753

28: High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells, Beumer, J; Puschhof, J; Bauza-Martinez, J et al., Cell, 2020, 181 (6) 1291 +, doi:10.1016/j.cell.2020.04.036

29: A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin, Sem Tamara, Vojtech Franc,Albert J. R. Heck, Proceedings of the National Academy of Sciences Jul 2020, 117 (27) 15554-15564; DOI: 10.1073/pnas.2002483117

30: A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface, Bäckström A, Kugel L, Gnann C, hao Xu, joseph E. Aslan, Emma Lundberg, Charlotte Stadler, J Histochem & Cytochem. 2020;68(7):473-489. doi:10.1369/0022155420935403

31: Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry, Barbara Steigenberger, Henk W.P. van den Toorn, Jean Francios Greisch, Emiel Bijl, Oliver Raether, Markus Lubeck, Albert J.R. Heck, Richard A. Scheltema, Jul 2020, MCP, doi: 10.1074/mcp.RA120.002094.

32: Platelet factor 4 is a biomarker for lymphatic-promoted disorders, Wanshu Ma, Hyea Jin Gil, Noelia Escobedo, Alberto Benito-Martín, Pilar Ximénez-Embún, Javier Muñoz, Héctor Peinado, Stanley G. Rockson, and Guillermo Oliver, JCI Insight, June 11 2020, 5(13):e13510, doi: 10.1172/jci.insight.135109

33: Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation, Sara C. Buch-Larsen, Ivo A. Hendriks, Jean M. Lodge et al., Cell Reports, 2020, (12) 108176 doi: 10.1016/j.celrep.2020.108176

34: The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensors, Tobias Hochstoeger, Tarek Al Said, Dante Maestre et al., Science Advances, 12 Aug 2020, doi: 10.1126/sciadv.abb9110

35: A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes, Piazza I, Beaton N, Bruderer R, et al., Nat Commun. 2020, 17, 981–984, doi: 10.1038/s41467-020-18071 x

36: MassIVE.qant: a community resource of quantitative mass spectrometry-based proteomics datasets, Choi M, Carver J, Chiva C, et al., Nat Methods17, 981–984 (2020). https://doi.org/10.1038/s41592-020-0955-0

37: Single-cell derived tumor organoids display diversity in HLA class I peptide presentation, Demmers, L.C., Kretzschmar, K., Van Hoeck, A, et al., Nat Commun 11, 5338 (2020), doi:10.1038/s41467-020-19142-9

38: Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling, Lilian M Fennell, Carlos Gomez Diaz, Luiza Deszcz, et al., EMBO Journal, 2020, 39:e103303, doi:10.15252/embj.2019103303

39: Feature-based molecular networking in the GNPS analysis environment, Nothias LF, Petras D, Schmid R, et al., Nat Methods 2020, 17, 905–908, doi:10.1038/s41592-020-0933-6

40: Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples, Noberini, R., Morales Torres, C, et al., J. Mol Sci., 2020, 21, 7330, doi: 10.3390/ijms21197330

41: Spatial proteomics defines the content of trafficking vesicles captured by golgin tethers, John J. H. Shin, Oliver M. Crook, Alicia C. Borgeaud et al., Nat Commun 11, 5987 (2020). https://doi.org/10.1038/s41467-020-19840-4