Publications

Open Access/Publications

All peer-reviewed scientific publications that stem from EPIC-XS project activities MUST BE OPEN ACCESS PUBLICATIONS.

All publications must properly acknowledge the project and the Horizon 2020 funding:

“This work has been supported by EPIC-XS, project number 823839, funded by the Horizon 2020 programme of the European Union.”

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, First published on April 22, 2020, 19 (7) 1209-1219; DOI: 10.1074/mcp.RA119.001624, https://www.mcponline.org/content/early/2020/04/22/mcp.RA119.001624.ful5

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, Wutz, Gordana ;Ladurner, Rene ;St Hilaire, Brian Glenn; Stocsits, Roman R.; Nagasaka, Kota ; Pignard, Benoit; Sanborn, Adrian ; Tang, Wen; Varnai, Csilla ;  Ivanov, Miroslav P ; Schoenfelder, Stefan; van der Lelij, Petra; Huang, Xingfan; Durnberger, Gerhard ; Roitinger, Elisabeth; Mechtler, Karl; Davidson, Iain Finley; Fraser, Peter; Lieberman-Aiden, Erez; Peters, 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, Yasset Perez-Riverol, Jeremy J. Carver, Deepti J. Kundu, David Garc´ıa-Seisdedos, Andrew F. Jarnuczak, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama and Juan A. Vizca´ıno, Nucleic Acids Research, Vol. 48, Issue: D1 Pages: D1145-D1152, DOI: 10.1093/nar/gkz984. Published Jan 8 2020. https://academic.oup.com/nar/article/48/D1/D1145/5612546

14: Removing the Hidden Data Dependency of DIA with Predicted Spectral Libraries, Bart Van Puyvelde, Sander Willems, Ralf Gabriels, Simon Daled, Laura De Clerck, Sofie Vande Casteele, An Staes, Francis Impens, Dieter Deforce, Lennart Martens, Sven Degroeve, and Maarten Dhaenens, Proteomics 2020, 20, Issue 3-4, 1900306, DOI: 10.1002/pmic.201900306, Published Feb 2020, https://onlinelibrary.wiley.com/doi/full/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, Publication Date: 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, Patrick Leopold Rüther, Kyle L Fort, Tabiwang N Arrey, Alexander Harder, Alexander A. Makarov, Jesper V. Olsen, Molecular & Cellular Proteomics February 12, 2020, DOI: 10.1074/mcp.TIR119.001906; https://www.mcponline.org/content/early/2020/02/12/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. [Epub ahead of prin20

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, Ana Martinez del Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen, 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

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

Publications 2019

1: The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases, Juan Antonio VizcaínoPeter Kubiniok, Kevin A. KovalchikQing MaJérôme D. DuquetteIan MongrainEric W. DeutschBjoern PetersAlessandro SetteIsabelle Sirois and Etienne Caron,

2: Targeting proline in (phospho)proteomics,  Saar A. M. van der Laarse, Charlotte A. G. H. van Gelder, Marshall Bern, Michiel Akeroyd, Maurien M. A. Olsthoorn and Albert J. R. Heck, FEBS J., 2019 Dec  [PubMed] DOI: 10.1111/febs.15190. [Epub ahead of print]

3: ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion, Hulstaert N., Shofstahl J., Sachsenberg T., Walzer M., Barsnes H., Perez-Riverol Y. J Proteome Res., 2020 Jan 3;19(1):537-542. [PubMed] DOI: 10.1021/acs.jproteome.9b00328. Epub 2019 Dec 63

4: Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions, Silva A.S., Bouwmeester R., Martens L., Degroeve S., Bioinformatics, 2019 Dec 15;35(24):5243-5248. [PubMed] DOI: 10.1093/bioinformatics/btz383.

5: Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications; RobertaNoberini, CamillaRestellini, Evelyn OlivaSavoia, TizianaBonaldi, ELSIVER Methods,  [PubMed] DOI:  10.1016/j.ymeth.2019.10.001. [Epub ahead of print]

6: Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites, Lundby, Alicia; Franciosa, Giulia ; Emdal, Kristina B.; Refsgaard, Jan C.;Gnosa, Sebastian P.;Bekker-Jensen, Dorte B.; Secher, Anna ;Maurya, Svetlana R.; Paul, Indranil; Mendez, Blanca L.; Kelstrup, Christian D.; Francavilla, Chiara ; Kveiborg, Marie ; Montoya, Guillermo; Jensen, Lars J. ; Olsen, Jesper V. CELL, Volume: 179; Issue: 2;Pages: 543-+ [PubMed] Full article DOI: 10.1016/j.cell.2019.09.006

7: PhoX: An IMAC-Enrichable Cross-Linking Reagent, Steigenberger, Barbara; Pieters, Roland J. ; Heck, Albert J. R. ; Scheltema, Richard A. ACS Cent. Sci.; Sep 25;5(9):1514-1522.; [PubMed] DOI: 10.1021/acscentsci.9b00417

8: Cross-ID: Analysis and Visualization of Complex XL−MS-Driven, Protein Interaction Networks, Sebastiaan C. de Graaf, Oleg Klykov, Henk van den Toorn and Richard A. Scheltema, J. Proteome Res. 2019, 18, 642−651, [PubMed], DOI:10.1021/acs.jproteome.8b00

9: A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach; Tamara, S., Hoek, M., Scheltema, RA, Leney AC., Heck, AJR, CHEM 2019, Vol 5, Issue 5, 1302-1317, [Science Direct] DOI 0.1016/j.chempr.2019.03.009
10: Quantifying the impact of public omics data, Perez-Riverol, Yasset; Zorin, Andrey; Dass, Gaurhari; Manh-Tu Vu; Xu, Pan; Glont, Mihai; Vizcaino, Juan Antonio; Jarnuczak, Andrew F.; Petryszak, Robert; Ping, Peipei; Hermjakob, Henning; Nature Communications,Vol.10, Article no., 3512, [PubMed] DOI: 10.1038/s41467-019-11461-w0
11: Updated (MSPIP)-P-2 web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques, Gabriels, Ralf; Martens, Lennart; Degroeve, Sven; Nucleic Acids Res., Vol. 47,W1,W295-W299, [PubMed] DOI: 10.1093/nar/gkz299
12: N-terminal beta-strand underpins biochemical specialization of an ATG8 isoform, Zess, Erin K.; Jensen, Cassandra; Cruz-Mireles Neftaly; De la Concepcion, Juan Carlos; Sklenar, Jan; Stephani, Madlen; Imre, Richard; Roitinger, Elisabeth; Hughes, Richard; Belhaj, Khaoula; Mechtler, Karl; Menke, Frank L. H.;Bozkurt, Tolga; Banfield, Mark J.;Kamoun, Sophien; Maqbool, Abbas; Dagdas, Yasin F.; Plos Biology, Vol.17, 7, Art. No. e3000373, [PubMed] DOI: 10.1371/journal.pbio.3000373
13: Isotopologue Multipoint Calibration for Proteomics Biomarker Quantification in Clinical Practice, Chiva, Cristina; Pastor, Olga); Trilla-Fuertes, Lucia; Gamez-Pozo, Angelo ;Fresno Vara, Juan Angel; Sabido, Eduard, Anal. Chem., Vol 91, 8, 4934-4938, [PubMed] DOI: 10.1021/acs.analchem.8b05802

14: Phosphopeptide Fragmentation and Site Localization by Mass Spectrometry: An Update, Potel, Clement M.; Lemeer, Simone; Heck, Albert J. R., Anal. Chem., Vol. 91, 1, 126-141, [PubMed] DOI: 10.1021/acs.analchem.8b04746

15: Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes, Zeman, J; Itoh, Y; Kukacka, Z; Rosulek, M; Kavan, D; Kouba, T; Jansen, ME; Mohammad, MP; Novak, P; Valasek, LS; . 2019 Sep 5; 47(15): 8282 8300 [PubMed] doi: 10.1093/nar/gkz570

16: Proteases Immobilization for In Situ Time-Limited Proteolysis on MALDI; Rosulek, M ; Darebna, P; Pompach, P ; Slavata, L; Novak, P; Catalysts, Volume:9 Issue:10; [PubMed] DOI: 10.3390/catal9100833

17: Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography; Stadlmann, Johannes; Hudecz, Otto; Krssakova, Gabriela ; Ctortecka, Claudia; Van Raemdonck, Geert; Op De Beeck, Jeff; Desmet, Gert; Penninger, Josef M.;Jacobs, Paul ;Mechtler, Karl; ANALYTICAL CHEMISTRY, Volume:91, Issue:22, Pages:14203-14207 [PubMed] DOI: 10.1021/acs.analchem.9b02899

18: Absolute quantification of cohesin, CTCF and their regulators in human cells; Holzmann, Johann; Politi, Antonio Z.; Nagasaka, Kota ; Hantsche-Grininger, Merle; Walther, Nike ;Koch, Birgit ; Fuchs, Johannes ; Duernberger, Gerhard; Tang, Wen; Ladurner, Rene; Stocsits, Roman R.;Busslinger, Georg A.; Novak, Bela; Mechtler, Karl;(Davidson, Iain Finley; Ellenberg, Jan; Peters, Jan-Michael; ELIFE, Volume:8 [PubMed] DOI: 10.7554/eLife.46269

19: MS-Based Approaches Enable the Structural Characterization of of Transcription Factor/DNA Response Element Complex; Slavata, Lukas ; Chmelik, Josef ;Kavan, Daniel ; Filandrova, Ruzena; Fiala, Jan ;Rosulek, Michal ; Mrazek, Hynek; Kukacka, Zdenek; Valis, Karel ; Man, Petr; Miller, Michael; McIntyre, William; Fabris, Daniele ;Novak, Petr; BIOMOLECULES, Volume:9, Issue:10, [PubMed] DOI: 10.3390/biom9100535

20. Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome, Kaige Yan, Jing Yang, Ziguo Zhang, Stephen H. McLaughlin, Leifu Chang,Domenico Fasci, Ann E. Ehrenhofer-Murray, Albert J. R. Heck, David Barford, Nature. 2019 Oct 2. [PubMed] DOI: 10.1038/s41586-019-1609-1

EC-Funded Initiative

OpenAIRE, is an EC funded initative designed to promote the open access policies of the EC and helps researchers, research officers and project coordinators comply with them.

EPIC-XS has its own page on OpenAIRE (EPIC-XS OpenAIRE), featuring project information, related project publications and datasets, and a statistics section. This information can be freely used for reporting purposes, generating tailor-made publication lists and statistics.