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Items: 31

1.

The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.

Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, Hulstaert N, Vandekerckhove J, Gevaert K, Martens L.

Nucleic Acids Res. 2013 Jan;41(Database issue):D333-7. doi: 10.1093/nar/gks998. Epub 2012 Oct 23.

2.

LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D246-51. doi: 10.1093/nar/gks915. Epub 2012 Oct 5.

3.

Sigpep: calculating unique peptide signature transition sets in a complete proteome background.

Helsens K, Mueller M, Hulstaert N, Martens L.

Proteomics. 2012 Apr;12(8):1142-6. doi: 10.1002/pmic.201100566.

PMID:
22577015
4.

Enabling computational proteomics by public and local data management systems.

Helsens K, Martens L.

Circ Cardiovasc Genet. 2012 Apr 1;5(2):266. doi: 10.1161/CIRCGENETICS.110.957837. No abstract available.

PMID:
22511708
5.

TraML--a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.

Mol Cell Proteomics. 2012 Apr;11(4):R111.015040. doi: 10.1074/mcp.R111.015040. Epub 2011 Dec 12.

6.

Analysis of the resolution limitations of peptide identification algorithms.

Colaert N, Degroeve S, Helsens K, Martens L.

J Proteome Res. 2011 Dec 2;10(12):5555-61. doi: 10.1021/pr200913a. Epub 2011 Oct 26.

PMID:
21995378
7.

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L.

J Proteome Res. 2011 Nov 4;10(11):5260-3. doi: 10.1021/pr200664h. Epub 2011 Oct 13.

8.

NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation.

Van Damme P, Hole K, Pimenta-Marques A, Helsens K, Vandekerckhove J, Martinho RG, Gevaert K, Arnesen T.

PLoS Genet. 2011 Jul;7(7):e1002169. doi: 10.1371/journal.pgen.1002169. Epub 2011 Jul 7.

9.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L.

J Proteome Res. 2011 Aug 5;10(8):3840-3. doi: 10.1021/pr2005154. Epub 2011 Jul 11.

PMID:
21714566
10.

Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation.

Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, Gevaert K.

J Proteome Res. 2011 Aug 5;10(8):3578-89. doi: 10.1021/pr2002325. Epub 2011 Jun 20.

PMID:
21619078
11.

Mass spectrometry-driven proteomics: an introduction.

Helsens K, Martens L, Vandekerckhove J, Gevaert K.

Methods Mol Biol. 2011;753:1-27. doi: 10.1007/978-1-61779-148-2_1.

PMID:
21604112
12.

compomics-utilities: an open-source Java library for computational proteomics.

Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L.

BMC Bioinformatics. 2011 Mar 8;12:70. doi: 10.1186/1471-2105-12-70.

13.

A stringent approach to improve the quality of nitrotyrosine peptide identifications.

Ghesquière B, Helsens K, Vandekerckhove J, Gevaert K.

Proteomics. 2011 Mar;11(6):1094-8. doi: 10.1002/pmic.201000526. Epub 2011 Feb 7.

PMID:
21298788
14.

Probing the efficiency of proteolytic events by positional proteomics.

Plasman K, Van Damme P, Kaiserman D, Impens F, Demeyer K, Helsens K, Goethals M, Bird PI, Vandekerckhove J, Gevaert K.

Mol Cell Proteomics. 2011 Feb;10(2):M110.003301. doi: 10.1074/mcp.M110.003301. Epub 2010 Nov 3.

15.

A quantitative proteomics design for systematic identification of protease cleavage events.

Impens F, Colaert N, Helsens K, Ghesquière B, Timmerman E, De Bock PJ, Chain BM, Vandekerckhove J, Gevaert K.

Mol Cell Proteomics. 2010 Oct;9(10):2327-33. doi: 10.1074/mcp.M110.001271. Epub 2010 Jul 13.

16.

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
17.

MS-driven protease substrate degradomics.

Impens F, Colaert N, Helsens K, Plasman K, Van Damme P, Vandekerckhove J, Gevaert K.

Proteomics. 2010 Mar;10(6):1284-96. doi: 10.1002/pmic.200900418. Review. Erratum in: Proteomics. 2010 Jul;10(13):2560.

PMID:
20058249
18.

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
19.

Rover: a tool to visualize and validate quantitative proteomics data from different sources.

Colaert N, Helsens K, Impens F, Vandekerckhove J, Gevaert K.

Proteomics. 2010 Mar;10(6):1226-9. doi: 10.1002/pmic.200900379.

PMID:
20058247
20.

Improved visualization of protein consensus sequences by iceLogo.

Colaert N, Helsens K, Martens L, Vandekerckhove J, Gevaert K.

Nat Methods. 2009 Nov;6(11):786-7. doi: 10.1038/nmeth1109-786. No abstract available.

PMID:
19876014
21.

Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity.

Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P.

Mol Cell Proteomics. 2009 Dec;8(12):2700-14. doi: 10.1074/mcp.M900310-MCP200. Epub 2009 Sep 16.

22.

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. doi: 10.1074/mcp.M900259-MCP200. Epub 2009 Sep 9.

23.

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).

Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.

Proteomics. 2009 Aug;9(15):3928-33. doi: 10.1002/pmic.200900247.

PMID:
19637238
24.

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans.

Arnesen T, Van Damme P, Polevoda B, Helsens K, Evjenth R, Colaert N, Varhaug JE, Vandekerckhove J, Lillehaug JR, Sherman F, Gevaert K.

Proc Natl Acad Sci U S A. 2009 May 19;106(20):8157-62. doi: 10.1073/pnas.0901931106. Epub 2009 May 6.

25.

Peptizer, a tool for assessing false positive peptide identifications and manually validating selected results.

Helsens K, Timmerman E, Vandekerckhove J, Gevaert K, Martens L.

Mol Cell Proteomics. 2008 Dec;7(12):2364-72. doi: 10.1074/mcp.M800082-MCP200. Epub 2008 Jul 30.

26.

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
27.

Human Proteinpedia enables sharing of human protein data.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A.

Nat Biotechnol. 2008 Feb;26(2):164-7. doi: 10.1038/nbt0208-164. No abstract available.

28.

Implementation and application of a versatile clustering tool for tandem mass spectrometry data.

Flikka K, Meukens J, Helsens K, Vandekerckhove J, Eidhammer I, Gevaert K, Martens L.

Proteomics. 2007 Sep;7(18):3245-58.

PMID:
17708593
29.

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
30.

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
31.

MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.

Helsens K, Martens L, Vandekerckhove J, Gevaert K.

Proteomics. 2007 Feb;7(3):364-6.

PMID:
17203510

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