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Items: 1 to 50 of 56

1.

An update on the moFF Algorithm for label-free quantitative proteomics.

Argentini A, Staes A, Grüning BA, Mehta S, Easterly C, Griffin TJ, Jagtap P, Impens F, Martens L.

J Proteome Res. 2018 Dec 4. doi: 10.1021/acs.jproteome.8b00708. [Epub ahead of print]

PMID:
30511867
2.

Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation.

Bruning U, Morales-Rodriguez F, Kalucka J, Goveia J, Taverna F, Queiroz KCS, Dubois C, Cantelmo AR, Chen R, Loroch S, Timmerman E, Caixeta V, Bloch K, Conradi LC, Treps L, Staes A, Gevaert K, Tee A, Dewerchin M, Semenkovich CF, Impens F, Schilling B, Verdin E, Swinnen JV, Meier JL, Kulkarni RA, Sickmann A, Ghesquière B, Schoonjans L, Li X, Mazzone M, Carmeliet P.

Cell Metab. 2018 Dec 4;28(6):866-880.e15. doi: 10.1016/j.cmet.2018.07.019. Epub 2018 Aug 23.

PMID:
30146486
3.

Evolutionarily conserved and species-specific glycoproteins in the N-glycoproteomes of diverse insect species.

Scheys F, Van Damme EJM, De Schutter K, Staes A, Gevaert K, Smagghe G.

Insect Biochem Mol Biol. 2018 Sep;100:22-29. doi: 10.1016/j.ibmb.2018.04.011. Epub 2018 Jun 12.

PMID:
29906502
4.

Chronic Kidney Disease Circulating Calciprotein Particles and Extracellular Vesicles Promote Vascular Calcification: A Role for GRP (Gla-Rich Protein).

Viegas CSB, Santos L, Macedo AL, Matos AA, Silva AP, Neves PL, Staes A, Gevaert K, Morais R, Vermeer C, Schurgers L, Simes DC.

Arterioscler Thromb Vasc Biol. 2018 Mar;38(3):575-587. doi: 10.1161/ATVBAHA.117.310578. Epub 2018 Jan 4.

PMID:
29301790
5.

Quality control in mass spectrometry-based proteomics.

Bittremieux W, Tabb DL, Impens F, Staes A, Timmerman E, Martens L, Laukens K.

Mass Spectrom Rev. 2018 Sep;37(5):697-711. doi: 10.1002/mas.21544. Epub 2017 Sep 7. Review.

PMID:
28802010
6.

Expanding the Interactome of TES by Exploiting TES Modules with Different Subcellular Localizations.

Sala S, Van Troys M, Medves S, Catillon M, Timmerman E, Staes A, Schaffner-Reckinger E, Gevaert K, Ampe C.

J Proteome Res. 2017 May 5;16(5):2054-2071. doi: 10.1021/acs.jproteome.7b00034. Epub 2017 Apr 20.

PMID:
28378594
7.

Protease Substrate Profiling by N-Terminal COFRADIC.

Staes A, Van Damme P, Timmerman E, Ruttens B, Stes E, Gevaert K, Impens F.

Methods Mol Biol. 2017;1574:51-76. doi: 10.1007/978-1-4939-6850-3_5.

PMID:
28315243
8.

moFF: a robust and automated approach to extract peptide ion intensities.

Argentini A, Goeminne LJ, Verheggen K, Hulstaert N, Staes A, Clement L, Martens L.

Nat Methods. 2016 Nov 29;13(12):964-966. doi: 10.1038/nmeth.4075. No abstract available.

PMID:
27898063
9.

De novo design of a biologically active amyloid.

Gallardo R, Ramakers M, De Smet F, Claes F, Khodaparast L, Khodaparast L, Couceiro JR, Langenberg T, Siemons M, Nyström S, Young LJ, Laine RF, Young L, Radaelli E, Benilova I, Kumar M, Staes A, Desager M, Beerens M, Vandervoort P, Luttun A, Gevaert K, Bormans G, Dewerchin M, Van Eldere J, Carmeliet P, Vande Velde G, Verfaillie C, Kaminski CF, De Strooper B, Hammarström P, Nilsson KP, Serpell L, Schymkowitz J, Rousseau F.

Science. 2016 Nov 11;354(6313). pii: aah4949.

10.

The Arabidopsis Iron-Sulfur Protein GRXS17 is a Target of the Ubiquitin E3 Ligases RGLG3 and RGLG4.

Nagels Durand A, Iñigo S, Ritter A, Iniesto E, De Clercq R, Staes A, Van Leene J, Rubio V, Gevaert K, De Jaeger G, Pauwels L, Goossens A.

Plant Cell Physiol. 2016 Sep;57(9):1801-13. doi: 10.1093/pcp/pcw122. Epub 2016 Aug 6.

PMID:
27497447
11.

The Response of the Root Proteome to the Synthetic Strigolactone GR24 in Arabidopsis.

Walton A, Stes E, Goeminne G, Braem L, Vuylsteke M, Matthys C, De Cuyper C, Staes A, Vandenbussche J, Boyer FD, Vanholme R, Fromentin J, Boerjan W, Gevaert K, Goormachtig S.

Mol Cell Proteomics. 2016 Aug;15(8):2744-55. doi: 10.1074/mcp.M115.050062. Epub 2016 Jun 17.

12.

CEP5 and XIP1/CEPR1 regulate lateral root initiation in Arabidopsis.

Roberts I, Smith S, Stes E, De Rybel B, Staes A, van de Cotte B, Njo MF, Dedeyne L, Demol H, Lavenus J, Audenaert D, Gevaert K, Beeckman T, De Smet I.

J Exp Bot. 2016 Aug;67(16):4889-99. doi: 10.1093/jxb/erw231. Epub 2016 Jun 13.

13.

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics.

Vandemoortele G, Staes A, Gonnelli G, Samyn N, De Sutter D, Vandermarliere E, Timmerman E, Gevaert K, Martens L, Eyckerman S.

Sci Rep. 2016 Jun 6;6:27220. doi: 10.1038/srep27220.

14.

Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin.

Gistelinck C, Gioia R, Gagliardi A, Tonelli F, Marchese L, Bianchi L, Landi C, Bini L, Huysseune A, Witten PE, Staes A, Gevaert K, De Rocker N, Menten B, Malfait F, Leikin S, Carra S, Tenni R, Rossi A, De Paepe A, Coucke P, Willaert A, Forlino A.

Sci Rep. 2016 Feb 15;6:21540. doi: 10.1038/srep21540.

15.

Protein aggregation as an antibiotic design strategy.

Bednarska NG, van Eldere J, Gallardo R, Ganesan A, Ramakers M, Vogel I, Baatsen P, Staes A, Goethals M, Hammarström P, Nilsson KP, Gevaert K, Schymkowitz J, Rousseau F.

Mol Microbiol. 2016 Mar;99(5):849-65. doi: 10.1111/mmi.13269. Epub 2015 Dec 9.

16.

Open-Source, Platform-Independent Library and Online Scripting Environment for Accessing Thermo Scientific RAW Files.

Kelchtermans P, Silva AS, Argentini A, Staes A, Vandenbussche J, Laukens K, Valkenborg D, Martens L.

J Proteome Res. 2015 Nov 6;14(11):4940-3. doi: 10.1021/acs.jproteome.5b00778. Epub 2015 Oct 29.

PMID:
26477298
17.

Study of Protein Expression in Peri-Infarct Tissue after Cerebral Ischemia.

Brea D, Agulla J, Staes A, Gevaert K, Campos F, Sobrino T, Blanco M, Dávalos A, Castillo J, Ramos-Cabrer P.

Sci Rep. 2015 Jul 8;5:12030. doi: 10.1038/srep12030.

18.

GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis.

Wrzaczek M, Vainonen JP, Stael S, Tsiatsiani L, Help-Rinta-Rahko H, Gauthier A, Kaufholdt D, Bollhöner B, Lamminmäki A, Staes A, Gevaert K, Tuominen H, Van Breusegem F, Helariutta Y, Kangasjärvi J.

EMBO J. 2015 Jan 2;34(1):55-66. doi: 10.15252/embj.201488582. Epub 2014 Nov 14.

19.

Citrullinated glucose-regulated protein 78 is an autoantigen in type 1 diabetes.

Rondas D, Crèvecoeur I, D'Hertog W, Ferreira GB, Staes A, Garg AD, Eizirik DL, Agostinis P, Gevaert K, Overbergh L, Mathieu C.

Diabetes. 2015 Feb;64(2):573-86. doi: 10.2337/db14-0621. Epub 2014 Sep 9.

20.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

21.

Asn3, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS.

Staes A, Vandenbussche J, Demol H, Goethals M, Yilmaz Ş, Hulstaert N, Degroeve S, Kelchtermans P, Martens L, Gevaert K.

Anal Chem. 2013 Nov 19;85(22):11054-60. doi: 10.1021/ac4027093. Epub 2013 Nov 4.

PMID:
24134513
22.

The Arabidopsis metacaspase9 degradome.

Tsiatsiani L, Timmerman E, De Bock PJ, Vercammen D, Stael S, van de Cotte B, Staes A, Goethals M, Beunens T, Van Damme P, Gevaert K, Van Breusegem F.

Plant Cell. 2013 Aug;25(8):2831-47. doi: 10.1105/tpc.113.115287. Epub 2013 Aug 20.

23.

SCX charge state selective separation of tryptic peptides combined with 2D-RP-HPLC allows for detailed proteome mapping.

Betancourt LH, De Bock PJ, Staes A, Timmerman E, Perez-Riverol Y, Sanchez A, Besada V, Gonzalez LJ, Vandekerckhove J, Gevaert K.

J Proteomics. 2013 Oct 8;91:164-71. doi: 10.1016/j.jprot.2013.06.033. Epub 2013 Jul 11.

PMID:
23851314
24.

Matrix metalloproteinase 13 modulates intestinal epithelial barrier integrity in inflammatory diseases by activating TNF.

Vandenbroucke RE, Dejonckheere E, Van Hauwermeiren F, Lodens S, De Rycke R, Van Wonterghem E, Staes A, Gevaert K, López-Otin C, Libert C.

EMBO Mol Med. 2013 Jul;5(7):1000-16. doi: 10.1002/emmm.201202100. Epub 2013 May 30.

25.

Proteomic and metabolomic responses to connexin43 silencing in primary hepatocyte cultures.

Vinken M, Maes M, Cavill R, Valkenborg D, Ellis JK, Decrock E, Leybaert L, Staes A, Gevaert K, Oliveira AG, Menezes GB, Cogliati B, Dagli ML, Ebbels TM, Witters E, Keun HC, Vanhaecke T, Rogiers V.

Arch Toxicol. 2013 May;87(5):883-94. doi: 10.1007/s00204-012-0994-0. Epub 2012 Dec 7.

PMID:
23224291
26.

A catalogue of putative HIV-1 protease host cell substrates.

Impens F, Timmerman E, Staes A, Moens K, Ariën KK, Verhasselt B, Vandekerckhove J, Gevaert K.

Biol Chem. 2012 Sep;393(9):915-31. doi: 10.1515/hsz-2012-0168.

PMID:
22944692
27.

The effect of peptide identification search algorithms on MS2-based label-free protein quantification.

Degroeve S, Staes A, De Bock PJ, Martens L.

OMICS. 2012 Sep;16(9):443-8. doi: 10.1089/omi.2011.0137. Epub 2012 Jul 17.

28.

Chromatographic retention time prediction for posttranslationally modified peptides.

Moruz L, Staes A, Foster JM, Hatzou M, Timmerman E, Martens L, Käll L.

Proteomics. 2012 Apr;12(8):1151-9. doi: 10.1002/pmic.201100386.

PMID:
22577017
29.

Cells lacking β-actin are genetically reprogrammed and maintain conditional migratory capacity.

Tondeleir D, Lambrechts A, Müller M, Jonckheere V, Doll T, Vandamme D, Bakkali K, Waterschoot D, Lemaistre M, Debeir O, Decaestecker C, Hinz B, Staes A, Timmerman E, Colaert N, Gevaert K, Vandekerckhove J, Ampe C.

Mol Cell Proteomics. 2012 Aug;11(8):255-71. doi: 10.1074/mcp.M111.015099. Epub 2012 Mar 22.

30.

How many spots with missing values can be tolerated in quantitative two-dimensional gel electrophoresis when applying univariate statistics?

Zellner M, Graf A, Zehetmayer S, Winkler W, Staes A, Gevaert K, Vandekerckhove J, Marchetti-Deschmann M, Miller I, Bauer P, Allmaier G, Oehler R.

J Proteomics. 2012 Mar 16;75(6):1792-802. doi: 10.1016/j.jprot.2011.12.019. Epub 2011 Dec 30.

PMID:
22227400
31.

cIAP1/2 are direct E3 ligases conjugating diverse types of ubiquitin chains to receptor interacting proteins kinases 1 to 4 (RIP1-4).

Bertrand MJ, Lippens S, Staes A, Gilbert B, Roelandt R, De Medts J, Gevaert K, Declercq W, Vandenabeele P.

PLoS One. 2011;6(9):e22356. doi: 10.1371/journal.pone.0022356. Epub 2011 Sep 12.

32.

Selecting protein N-terminal peptides by combined fractional diagonal chromatography.

Staes A, Impens F, Van Damme P, Ruttens B, Goethals M, Demol H, Timmerman E, Vandekerckhove J, Gevaert K.

Nat Protoc. 2011 Jul 14;6(8):1130-41. doi: 10.1038/nprot.2011.355.

PMID:
21799483
33.

Combining quantitative proteomics data processing workflows for greater sensitivity.

Colaert N, Van Huele C, Degroeve S, Staes A, Vandekerckhove J, Gevaert K, Martens L.

Nat Methods. 2011 Jun;8(6):481-3. doi: 10.1038/nmeth.1604. Epub 2011 May 8.

PMID:
21552256
34.

Complementary positional proteomics for screening substrates of endo- and exoproteases.

Van Damme P, Staes A, Bronsoms S, Helsens K, Colaert N, Timmerman E, Aviles FX, Vandekerckhove J, Gevaert K.

Nat Methods. 2010 Jul;7(7):512-5. doi: 10.1038/nmeth.1469. Epub 2010 Jun 6.

PMID:
20526345
35.

ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L.

Proteomics. 2010 Mar;10(6):1261-4. doi: 10.1002/pmic.200900409. Erratum in: Proteomics.2010 Jul;10(13):2560.

PMID:
20058248
36.

Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster.

Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E.

PLoS Biol. 2009 Nov;7(11):e1000236. doi: 10.1371/journal.pbio.1000236. Epub 2009 Nov 3.

37.

Analysis of the gamma-secretase interactome and validation of its association with tetraspanin-enriched microdomains.

Wakabayashi T, Craessaerts K, Bammens L, Bentahir M, Borgions F, Herdewijn P, Staes A, Timmerman E, Vandekerckhove J, Rubinstein E, Boucheix C, Gevaert K, De Strooper B.

Nat Cell Biol. 2009 Nov;11(11):1340-6. doi: 10.1038/ncb1978. Epub 2009 Oct 18.

PMID:
19838174
38.

A review of COFRADIC techniques targeting protein N-terminal acetylation.

Van Damme P, Van Damme J, Demol H, Staes A, Vandekerckhove J, Gevaert K.

BMC Proc. 2009 Aug 4;3 Suppl 6:S6. doi: 10.1186/1753-6561-3-S6-S6.

39.

The tandem PDZ protein Syntenin interacts with the aminoacyl tRNA synthetase complex in a lysyl-tRNA synthetase-dependent manner.

Meerschaert K, Remue E, De Ganck A, Staes A, Boucherie C, Gevaert K, Vandekerckhove J, Kleiman L, Gettemans J.

J Proteome Res. 2008 Nov;7(11):4962-73. doi: 10.1021/pr800325u. Epub 2008 Oct 8.

PMID:
18839981
40.

Multiple isoforms of the tumor suppressor myopodin are simultaneously transcribed in cancer cells.

De Ganck A, De Corte V, Staes A, Gevaert K, Vandekerckhove J, Gettemans J.

Biochem Biophys Res Commun. 2008 May 30;370(2):269-73. doi: 10.1016/j.bbrc.2008.03.086. Epub 2008 Mar 25.

PMID:
18371299
41.

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC).

Staes A, Van Damme P, Helsens K, Demol H, Vandekerckhove J, Gevaert K.

Proteomics. 2008 Apr;8(7):1362-70. doi: 10.1002/pmic.200700950.

PMID:
18318009
42.

A new approach for mapping sialylated N-glycosites in serum proteomes.

Ghesquière B, Buyl L, Demol H, Van Damme J, Staes A, Timmerman E, Vandekerckhove J, Gevaert K.

J Proteome Res. 2007 Nov;6(11):4304-12. Epub 2007 Oct 5.

PMID:
17918875
43.

Assessing a novel microfluidic interface for shotgun proteome analyses.

Staes A, Timmerman E, Van Damme J, Helsens K, Vandekerckhove J, Vollmer M, Gevaert K.

J Sep Sci. 2007 Jul;30(10):1468-76.

PMID:
17623427
44.

Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis.

Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, Klein C, Martens L, Staes A, Timmerman E, Van Damme J, Siedler F, Pfeiffer F, Vandekerckhove J, Oesterhelt D.

J Proteome Res. 2007 Jun;6(6):2195-204. Epub 2007 Apr 20.

PMID:
17444671
45.

A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes.

Hanoulle X, Van Damme J, Staes A, Martens L, Goethals M, Vandekerckhove J, Gevaert K.

J Proteome Res. 2006 Dec;5(12):3438-45.

PMID:
17137346
46.

Improved tandem mass spectrometric characterization of 3-nitrotyrosine sites in peptides.

Ghesquière B, Goethals M, Van Damme J, Staes A, Timmerman E, Vandekerckhove J, Gevaert K.

Rapid Commun Mass Spectrom. 2006;20(19):2885-93.

PMID:
16941724
47.

Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells.

Gevaert K, Pinxteren J, Demol H, Hugelier K, Staes A, Van Damme J, Martens L, Vandekerckhove J.

J Proteome Res. 2006 Jun;5(6):1415-28.

PMID:
16739993
48.

Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis.

Van Damme P, Martens L, Van Damme J, Hugelier K, Staes A, Vandekerckhove J, Gevaert K.

Nat Methods. 2005 Oct;2(10):771-7.

PMID:
16179924
49.

Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC.

Gevaert K, Staes A, Van Damme J, De Groot S, Hugelier K, Demol H, Martens L, Goethals M, Vandekerckhove J.

Proteomics. 2005 Sep;5(14):3589-99.

PMID:
16097034
50.

The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile.

Martens L, Van Damme P, Van Damme J, Staes A, Timmerman E, Ghesquière B, Thomas GR, Vandekerckhove J, Gevaert K.

Proteomics. 2005 Aug;5(12):3193-204.

PMID:
16038019

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