1: The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases, , , , , , , , , , and
Publications 2019
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: 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; Nucleic Acids Res. 2019 Sep 5; 47(15): 8282 8300 [PubMed] doi: 10.1093/nar/gkz570
15: 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
16: 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
17: 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
18: 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