Publications
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):1130-1141 PMID: 19741252
In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography.
Ghesquière B, Colaert N, Helsens K, Dejager L, Vanhaute C, Verleysen K, Kas K, Timmerman E, Goethals M, Libert C, Vandekerckhove J, Gevaert K.
Mol Cell Proteomics. 2009 Dec;8(12):2642-52. Epub 2009 Sep 9. PMID: 19741252
Highly efficient peptide separations in proteomics. Part 2: bi- and multidimensional liquid-based separation techniques.
Sandra K, Moshir M, D’hondt F, Tuytten R, Verleysen K, Kas K, François I, Sandra P.
J Chromatogr B Analyt Technol Biomed Life Sci. 2009 Apr 15;877(11-12):1019-39. Epub 2009 Feb 27. Review. PMID: 19297255
Application of a combined weak cation-exchange/crown ether column: first demonstrations of a versatile tool for proteome subselection.
Tuytten R, Ruttens B, Gheysen K, Sandra K, De Cremer K, Vlieghe D, Van Landuyt N, Thomas G, Martins JC, Sandra P, Kas K, Verleysen K.
Anal Chem. 2009 Apr 1;81(7):2456-69. PMID: 19275152
Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs.
Van Damme P, Maurer-Stroh S, Plasman K, Van Durme J, Colaert N, Timmerman E, De Bock PJ, Goethals M, Rousseau F, Schymkowitz J, Vandekerckhove J, Gevaert K.
Mol Cell Proteomics. 2009 Feb;8(2):258-72. Epub 2008 Oct 3. PMID:18836177
Highly efficient peptide separations in proteomics Part 1. Unidimensional high performance liquid chromatography.
Sandra K, Moshir M, D’hondt F, Verleysen K, Kas K, Sandra P.
J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Apr 15;866(1-2):48-63. Epub 2007 Oct 30. Review. PMID: 18006394
Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach.
Valkenborg D, Assam P, Thomas G, Krols L, Kas K, Burzykowski T.
Rapid Commun Mass Spectrom. 2007;21(20):3387-91. PMID:17891751
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
A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography.
Valkenborg D, Thomas G, Krols L, Kas K, Burzykowski T.
J Mass Spectrom. 2009 Apr;44(4):516-29. PMID:19065607
A la carte proteomics with an emphasis on gel-free techniques.
Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J.
Proteomics. 2007 Aug;7(16):2698-718. Review. PMID:17640001
Caspase-14 protects against epidermal UVB photodamage and water loss.
Denecker G, Hoste E, Gilbert B, Hochepied T, Ovaere P, Lippens S, Van den Broecke C, Van Damme P, D’Herde K, Hachem JP, Borgonie G, Presland RB, Schoonjans L, Libert C, Vandekerckhove J, Gevaert K, Vandenabeele P, Declercq W.
Nat Cell Biol. 2007 Jun;9(6):666-74. Epub 2007 May 21. PMID:17515931
Combination of COFRADIC® and high temperature-extended column length conventional liquid chromatography: a very efficient way to tackle complex protein samples, such as serum.
Sandra K, Verleysen K, Labeur C, Vanneste L, D’Hondt F, Thomas G, Kas K, Gevaert K, Vandekerckhove J, Sandra P.
J Sep Sci. 2007 Mar;30(5):658-68. PMID:17461103
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
Proteome-wide Identification of HtrA2/Omi Substrates.
Vande Walle L, Van Damme P, Lamkanfi M, Saelens X, Vandekerckhove J, Gevaert K, Vandenabeele P.
J Proteome Res. 2007 Mar;6(3):1006-15. Epub 2007 Feb 1. PMID:17266347
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
Proteome-wide characterization of N-glycosylation events by diagonal chromatography.
Ghesquière B, Van Damme J, Martens L, Vandekerckhove J, Gevaert K.
J Proteome Res. 2006 Sep;5(9):2438-47. PMID:16944957
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
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
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering.
Flikka K, Martens L, Vandekerckhove J, Gevaert K, Eidhammer I.
Proteomics. 2006 Apr;6(7):2086-94. PMID:16518876
Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?
Gevaert K, Van Damme P, Martens L, Vandekerckhove J.
Anal Biochem. 2005 Oct 1;345(1):18-29. Epub 2005 Mar 14. Review. PMID:16181830
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
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
PRIDE: the proteomics identifications database.
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R.
Proteomics. 2005 Aug;5(13):3537-45. Erratum in: Proteomics. 2005 Oct;5(15):4046. PMID: 16041671
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K.
Proteomics. 2005 Aug;5(13):3501-5. PMID:16041670
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
DBToolkit: processing protein databases for peptide-centric proteomics.
Martens L, Vandekerckhove J, Gevaert K.
Bioinformatics. 2005 Sep 1;21(17):3584-5. Epub 2005 Jul 19. PMID:16030071
On the technicalities of discovering and applying protein biomarkers for cancer prevention.
Kas K.
Eur J Cancer Prev. 2004 Oct;13(5):437-46. Review. PMID:15452457
Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18.
Staes A, Demol H, Van Damme J, Martens L, Vandekerckhove J, Gevaert K.
J Proteome Res. 2004 Jul-Aug;3(4):786-91. PMID:15359732
Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies.
Gevaert K, Ghesquière B, Staes A, Martens L, Van Damme J, Thomas GR, Vandekerckhove J.
Proteomics. 2004 Apr;4(4):897-908. PMID:15048972
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.
Gevaert K, Goethals M, Martens L, Van Damme J, Staes A, Thomas GR, Vandekerckhove J.
Nat Biotechnol. 2003 May;21(5):566-9. Epub 2003 Mar 31. PMID:12665801
Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins.
Gevaert K, Van Damme J, Goethals M, Thomas GR, Hoorelbeke B, Demol H, Martens L, Puype M, Staes A, Vandekerckhove J.
Mol Cell Proteomics. 2002 Nov;1(11):896-903. PMID:12488465