Publications

Open Access/Publications

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

 

Guidelines on Open Access Guidelines to to Scientific Publications and Open Access to Research Data in Horizon 2020 are available here:   Guidelines on open access

 

Make sure that all publications resulting from EPIC-XS 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: 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, 17 March 2020, DOI/10.1021/acsomega.0c00080, https://pubs.acs.org/doi/10.1021/acsomega.0c00080

2: 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.

3: 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]

4: 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

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: TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells, Rubin Narayan Joshi, Charlotte Stadler, Robert Lehmann, Janne Lehtiö, Jesper Tegnér, Angelika Schmidt and Mattias Vesterlund, Front. Immunol., 26 November 2019, https://doi.org/10.3389/fimmu.2019.02708

4: 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 6.

5: 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.

6: 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]

7: 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.2019.09.008

8: 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.9b00416

9*: 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

10: 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.8b0072

11: 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.2019.03.006 
12: 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-w
13: 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
14: 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
15: 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

16: 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

17: 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

18: 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

19: 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

20: 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

21: 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

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.