Publications

2017

• A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation
  De Vijlder T., Valkenborg D., Lemière F., Romijn EP., Laukens K., Cuyckens F. (2017) Mass Spectrom Rev. Nov 9; doi: 10.1002/mas.21551.
   
• Candiate biomarkers in the cervcial vaginal fluid for the (self-)diagnosis of cervical precancer
  Van Ostade X., Dom M., Tjalma W., Van Raemdonck G. (2017) Arch Gynecol Obstet. Nov; doi: 10.1007/s00404-017-4587-2.
   
• InSourcer: a high-throughput method to search for unknown metabolite modifications by mass spectrometry
  Mrzic A., Lermyte F., Vu TN., Valkenborg D., Laukens K. (2017) Rapid Commun Mass Spectrom. Sep 15; 31(17): 1396-1404.
   
• Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
  Ciach MA., Lacki MK., Miasojedow B., Lermyte F., Valkenborg D., Sobott F., Gambin A. (2017) J Comput Biol., Sep 25; doi: 10.1089/cmb.2017.0156.
   
• Quantification of egg ovalbumin hydrolysate-derived anti-hypertensive peptides in an in vitro model combining luminal digestion with intestinal Caco-2 cell transport
  Grootaert C., Jacobs G., Matthijs B., Pitart J., Baggerman G., Possemiers S., Van der Saag H., Smagghe G., Van Camp J., Voorspoels S. (2017) Food Res Int., Sep; 99(pt1): 531-541.
   
• Quality control in mass spectrometry-based proteomics
  Bittremieux W., Tabb DL., Impens F., Staes A., Timmerman E., Martens L., Laukens K. (2017) Rapid Commun Mass Spectrom. Sep 7; doi: 10.1002/mas.21544. 
   
• Protein complex analysis: From raw protein lists to protein interaction networks
  Meysman P., Titeca K., Eyckerman S., Tavernier J., Goethals B., Martens L., Valkenborg D., Laukens K. (2017) Rapid Commun Mass Spectrom. Sep; 36(5): 600-614.
   
• MS imaging and mass spectrometric synaptosome profiling identify PEP-19/pcp4 as a synaptic molecule involved in spatial learning in mice
  Aerts J., Laeremans A., Minerva L., Boonen K., Harshavardhan B., D'hooge R., Valkenborg D., Baggerman G., Arckens L. (2017) Biochim Biophys Acta, Jul; 1865(7):936-945.
   
• Analyzing complex mixtures of drug-like molecules: Ion mobility as an adjunct to existing liquid chromatography-(tandem) mass spectrometry methods
  Boschmans J., Lemière F., Sobott F. (2017) J Chromatography A, Mar 24; 1490:80-88.
   
• Peptidomics of the zebrafish Danio rerio: In search for neuropeptides
  Van Camp K., Baggerman G., Blust R., Husson S. (2017) J Proteomics, Jan 6; 150:290-296.

2016

• The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors
  Jonckheere W., Dermauw W., Zhurov V., Wybouw N., Van den Bulcke J., Villarroel CA., Greenhalgh R., Grbic M., Schuurink RC., Tirry L., Baggerman G., Clark RM., Kant MR., Vanholme B., Menschaert G., Van Leeuwen T. (2016) Mol Cell Protoemics, Dec 15; (12):3594-3613.
   
• Assessing the Immunosafety of Engineered Nanoparticles with a Novel in Vitro Model Based on Human Primary Monocytes
  Li Y., Italiani P., Casals E., Valkenborg D., Mertens I., Baggerman G., Nelissen I., Puntes VF., Boraschi D. (2016) ACS Appl Mater Interfaces, Oct 13.
   
• Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry
  Osbak KK., Houston S., Lithgow KV., Meehan CJ., Strouhal M., Smajs D., Cameron CE., Van Ostade X., Kenyon CR., Van Raemdonck GA. (2016) PLoS Negl Trop Dis, Sep 8; 10(9):e0004988
   
• Computational quality control tools for mass spectrometry proteomics
  Bittremieux W., Valkenborg D., Martens L., Laukens K. (2016) Proteomics, Aug 23; doi: 10.1002/pmic.201600159
   
• CONSTANd: a normalization method for isobaric labeled spectra by constrained optimization
  Maes E., Hadiwikarta W.W., Mertens I., Baggerman G., Hooyberghs J., Valkenborg D. (2016) Mol Cell Proteomics, Jun 14; mcp.M115.
   
• Designing biomedical proteomics experiments: state-of-the-art and future perspectives
  Maes E., Kelchtermans P., Bittremieux W., De Grave K., Degroeve S., Hooyberghs J., Mertens I., Baggerman G., Ramon J., Laukens K., Martens L., Valkenborg D. (2016) Expert Rev Proteomics, May, 13 (5); 495-511.
   
• The use of elemental mass spectrometry in phosphoproteomic applications
  Maes E., Tirez K., Baggerman G., Valkenborg D., Schoolfs L., Encinar J.R., Mertens I. (2016) Mass Spectrom Rev., May; 35(3): 350-60.
   
• Fast and Reliable Quantitative Peptidomics with labelpepmatch
  Verdonck R., De Haes W., Cardoen D., Menschaert G., Huhn T., Landuyt B., Baggerman G., Boonen K., Wenseleers T., Schoofs L. (2016) J Proteome Res., Mar 4; 15(3): 1080-9.
   
• Exosomal miRNA Analysis in Non-small Cell Lung Cancer (NSCLC) Patients' Plasma Through qPCR: A Feasible Liquid Biopsy Tool
  Giallombardo M., Chacártegui B.J., Castiglia M., Van Der Steen N., Mertens I., Pauwels P., Peeters M., Rolfo C. (2016) J Vis Exp., May 27;(111).
   
• Unsupervised Quality Assessment of Mass Spectrometry Proteomics Experimetns by Multivariate Quality Control Metrics
  Bittremieux W., Meysman P., Martens L., Valkenborg D., Laukens K. (2016) J Proteome Res, Apr 1; 15(4):1300-7.

2015

• The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides in the field of proteomics
  Maes E., Brusten W., Beutels F., Baggerman G., Mertens I., Valkenborg D., Landuyt B. Schoofs L., Tirez K. (2015) Rapid Commun. Mass Spectrometry, 29(1):35-44.
   
• Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments
  Maes E., Valkenborg D., Baggerman G., Schoofs L., Mertens I. (2015)  Plos One, 10(3):e0120115.
   
• Proteomics in cancer research: Are we ready for clinical practice?
  Maes E., Mertens I., Valkenborg D., Pauwels P., Rolfo C., Baggerman G. (2015)  Critical Reviews in Oncology/Hematology, S1040-8428(15), 30006-8.
   
• Proteomics applications in Caenorhabditis elegans research
  Husson S.J., Moyson S., Valkenborg D., Baggerman G., Mertens I. (2015) Biochem Biophys Res Commun, Dec 25;468(4):519-24
   
• An effectiveplasma membrane proteomics approach for small tissue samples
  Smolders K., Lombaert N., Valkenborg D., Baggerman G., Arckens L. (2015)  Sci Rep., Jun5;5:10917
   
• Translating clinical proteomics: the importanceof study design
  Maes E., Cho W.C., Baggerman G. (2015) Expert Rev Proteomics, Jun;12(3):217-9.
   
• Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments
  Maes E., Valkenborg D., Baggerman G., Willems H., Landuyt B., Schoofs L., Mertens I. (2015) PLoS One, Mar 16;10(3)
   
• The benefits and limitations of reaction cell and sector field inductively coupled plasma mass spectrometry in the detection and quantification of phosphopeptides
  Maes E., Brusten W., Beutels F., Baggerman G., Mertens I., Valkenborg D., Landuyt B., Schoofs L., Tirez K. (2015) Rapid Commun. Mass Spectrometry, Jan15;29(1):35-44.
   
• Protein complex analysis: From raw protein lists to protein interaction networks
  Meysman P., Titeca K., Eyckerman S., Tavernier J., Goethals B., Martens L., Valkenborg D., Laukens K. (2015) Mass Spectrom Rev., Dec 28.

2014

• Colorectal cancer biomarker discovery and validation using LCMS/MS based proteomics in blood: truth or dare?
  Reumer A., Maes E., Mertens I., Cho C.W., Landuyt B., Valkenborg D., Schoofs L., Baggerman G. (2014) Expert Rev Proteomics, 11(4), 449-63.
   
• Worm peptidomics
  Husson S.J., Reumer A., Temmerman L., De Haes W., Schoofs L., Mertens I., Baggerman G. (2014) EuPA OPEN PROTEOMICS, 3:280-290.
   
• Identification of protein biomarkers for cervical cancer using human cervicovaginal fluid
  Van Raemdonck G.A., Tjalma W.A., Coen E.P., Depuydt C.E., Van Ostade X.W. (2014) PLoS One, Sept 12;9(9) e:106488.
   
• Increased Serpin A5 levels in the cervicovaginal fluid of HIV-1 exposed seronegatives suggest that a subtle balance between serine protease and their inhibitors may determine susceptibility to HIV-1 infection
  Van Raemdonck G., Zegels G., Coen E., Vuylsteke B., Jennes W., Van Ostade X. (2014) Virology, June;458-459: 11-21.
   
• The use of elemental mass spectrometry in phosphoproteomic applications
  Maes E., Tirez K., Baggerman G., Valkenborg D., Schoofs L. , Encinar J.R., Mertens I. (2014) Mass Spectrom Rev. (doi: 10.1002/mas.21440).
   
• Liquid Biopsies in Lung Cancer:  The new Ambrosia of researchers
  Rolfo C.D., Castiglia M., Hong D., Alessandro R., Mertens I., Baggerman G., Zwaenepoel K., Gil-Bazo I., Passiglia F., Carreca A.P., Taverna S., Vento R., Santini D., Peeters M., Russo A., Pauwels P. (2014) BBA Cancer Rev., 1846 (2) 539–546.
   
• The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results
  Ghavidel F.Z., Mertens I., Baggerman G., Laukens K., Burzykowski T., Valkenborg D. (2014) J Proteomics, Feb 26;98:150-8

2013

• Interindividual variation in the proteome of human peripheral blood mononuclear cells
  Maes E., Landuyt B., Mertens I., Schoofs L. (2013) Plos One, 8, e61933.
   
• Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges and future prospectives
  Maes E., Broeckx V., Mertens I., Sagaert X., Prenen H., Landuyt B., Schoofs L. (2013) Amino Acids, 45 (2), 205-218.
   
• Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using Tandem Mass Tag protein labeling
  Maes E., Valkenborg  D., Mertens I., Broeckx, V., Baggerman G., Sagaert X., Landuyt B., Prenen H., Schoofs L. (2013). Mol Biosyst., 9(11),2686-2695.
   
• The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results
  Ghavidel F.Z., Mertens I., Baggerman G., Laukens K., Burzykowski T., Valkenborg D. (2013) J. Proteomics, 98, 150-8.
   
• Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
  Crappé J, Van Criekinge W, Trooskens G, Hayakawa E, Luyten W, Baggerman G, Menschaert G. (2013) BMC Genomics, Sep 23;14:648
   
• Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation
  Hayakawa E, Menschaert G, De Bock PJ, Luyten W, Gevaert K, Baggerman G, Schoofs L. (2013) J Proteome Res., Dec 6;12(12):5410-21
   
• Proteomic analysis of formalin-fixed paraffin-embedded colorectal cancer tissue using tandem mass tag protein labeling
  Maes E, Valkenborg D, Mertens I, Broeckx V, Baggerman G, Sagaert X, Landuyt B, Prenen H, Schoofs L. (2013) Mol Biosyst, Nov;9(11):2686-95
   
• Frog nuptial pads secrete mating season-specific proteins related to salamander pheromones
  Willaert B, Bossuyt F, Janssenswillen S, Adriaens D, Baggerman G, Matthijs S, Pauwels E, Proost P, Raepsaet A, Schoofs L, Stegen G, Treer D, Van Hoorebeke L,Vandebergh W, Van Bocxlaer I. (2013) J Exp Biol, Nov 15;216(Pt22):4139-4
   
• Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments
  Ejigu BA, Valkenborg D, Baggerman G, Vanaerschot M, Witters E, Dujardin JC, Burzykowski T, Berg M. (2013) OMICS, Sep;17(9):473-85
   
• Peptidomic analysis of human reflex tear fluid
  Hayakawa E, Landuyt B, Baggerman G, Cuyvers R, Lavigne R, Luyten W, Schoofs L. (2013) Peptides, Apr;42:63-9