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Publications

This list includes papers with co-authorship of IMSC-employed personnel: Hjalmar Permentier, Annie van Dam, Margot Jeronimus-Stratingh, Andries Bruins (former head of MS center, until 2010), as well as Marcel de Vries (seconded to IMSC from UMCG, from 2013).

2017

  • Gil A, Siegel D, Bonsing-Vedelaar S, Permentier H, Reijngoud DJ, Dekker F, Bischoff R. 2017. The degradation of nucleotide triphosphates extracted under boiling ethanol conditions is prevented by the yeast cellular matrix. Metabolomics 13(1): 1.
  • Han J, Schmidt A, Zhang T, Permentier H, Groothuis GMM, Bischoff R, Kühn FE, Horvatovich P, Casini A. 2017. Bioconjugation strategies to couple supramolecular exo-functionalized palladium cages to peptides for biomedical applications. Chemical Communications in press.

2016

  • Barata-Vallejo S, Ferreri C, Zhang T, Permentier H, Bischoff R, Bobrowski K, Chatgilialoglu C. 2016. Radiation Chemical Studies of Gly-Met-Gly in Aqueous Solution. Free Radical Research 1-32..
  • Bischoff R, Permentier H, Guryev V, Horvatovich P. 2016. Genomic variability and protein species - improving sequence coverage for proteogenomics. Journal of Proteomics 134:25-36.
  • van den Brink FTG, Zhang T, Ma L, Bomer J, Odijk M, Olthuis W, Permentier HP, Bischoff R, van den Berg A. 2016. Electrochemical protein cleavage in a microfluidic cell with integrated boron doped diamond electrodes. Analytical Chemistry 88:9190-9198.
  • van Eunen K, Volker-Touw CML, Gerding A, Bleeker A, Wolters JC, van Rijt WJ, Martines ACMF, Niezen-Koning KE, Heiner RM, Permentier H, Groen AK, Reijngoud DJ, Derks TGJ, Bakker BM. 2016. Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. BMC Biology 14:107.
  • Gul T, Krzek M, Permentier HP, Fraaije MW, Bischoff R. 2016. Microbial flavoprotein monooxygenases as mimics of mammalian flavin-containing monooxygenases for the enantioselective preparation of drug metabolites. Drug Metabolism and Disposition 44:1270-1276.
  • Krzek M, van Beek HL, Permentier HP, Bischoff R, Fraaije MW. 2016. Covalent immobilization of a flavoprotein monooxygenase via its flavin cofactor. Enzyme and Microbial Technology 82:138-143.
  • Le Thi Ngoc L, Yuan T, Oonishi N, van Nieuwkasteele J, van den Berg A, Permentier H, Bischoff R, Carlen ET. 2016. Suppression of surface-enhanced Raman scattering on gold nanostructures by metal adhesion layers. The Journal of Physical Chemistry. C: Nanomaterials and Interfaces 120(33):18756-18762.
  • Li M, de Graaf IAM, Siissalo S, de Jager MH, van Dam A, Groothuis GMM. 2016 The consequence of drug-drug interactions influencing the interplay between P-gp and Cyp3a: An ex vivo study with rat precision-cut intestinal slices. Drug Metabolism and Disposition 44(5):683-691.
  • Ruokolainen M, Gul T, Permentier H, Sikanen T, Kostiainen R, Kotiaho T. 2016. Comparison of TiO2 photocatalysis, electrochemically assisted Fenton reaction and direct electrochemistry for simulation of phase I metabolism reactions of drugs. European Journal of Pharmaceutical Sciences 83:36-44.
  • Wolters JC, Ciapaite J, van Eunen K, Niezen-Koning KE, Matton A, Porte RJ, Horvatovich P, Bakker BM, Bischoff R, Permentier HP. 2016. Translational targeted proteomics profiling of mitochondrial energy metabolic pathways in mouse and human samples. Journal of Proteome Research 15(9):3204-3213.
  • Zhang T, Niu X, Yuan T, Tessari M, de Vries MP, Permentier HP, Bischoff R. 2016. Efficient and selective chemical labeling of electrochemically generated peptides based on spirolactone chemistry. Analytical Chemistry 88:6465-6471.
  • Zhou L, Shao J, Li Q, van Heel AJ, de Vries MP, Broos J, Kuipers OP. 2016. Incorporation of tryptophan analogues into the lantibiotic nisin. Amino Acids 48(5):1309-1318.

2015

  • Baas BJ, Poddar H, Geertsema EM, Rozeboom HJ, de Vries MP, Permentier HP, Thunnisen AM, Poelarends GJ. 2015. Functional and structural characterization of an unusual cofactor-independent oxygenase. Biochemistry 54:1219-1232.
  • Gil A, Siegel D, Permentier H, Reijngoud DJ, Dekker F, Bischoff R. 2015. Stability of energy metabolites - An often overlooked issue in metabolomics studies: A review. Electrophoresis 36:2156-2169.
  • Gul T, Bischoff R, Permentier HP. 2015. Optimization of reaction parameters for the electrochemical oxidation of lidocaine with a Design of Experiments approach. Electrochimica Acta 171:23-28.
  • Gul T, Bischoff R, Permentier HP. 2015. Electrosynthesis methods and approaches for the preparative production of metabolites from parent drugs. TrAC-Trends in Analytical Chemistry 70:58-66.
  • Meijer K, Weening D, de Vries MP, Priebe MG, Vonk RJ, Roelofsen H. 2015. Quantitative proteomics analyses of activation states of human THP-1 macrophages. Journal of Proteomics 128:164-172.
  • Rahimi M, Ng EP, Bakhtiari K, Vinciguerra M, Ali Ahmad H, Awala H, Mintova S, Daghighi M, Bakhshandeh Rostami F, de Vries M, Motazacker MM, Peppelenbosch MP, Mahmoudi M, Rezaee F. 2015. Zeolite nanoparticles for selective sorption of plasma proteins. Scientific Reports 5:17259.
  • Sakulkhu U, Mahmoudi M, Maurizi L, Coullerez G, Hofmann-Amtenbrink M, de Vries M, Motazacker M, Rezaee F, Hofmann H. 2015. Significance of surface charge and shell material of superparamagnetic iron oxide nanoparticle (SPION) based core/shell nanoparticles on the composition of the protein corona. Biomaterials Science 3:265-278.
  • Yuan T, Le Thi Ngoc L, van Nieuwkasteele J, Odijk M, van den Berg A, Permentier H, Bischoff R, Carlen ET. 2015. In situ surface-enhanced Raman spectroelectrochemical analysis system with a hemin modified nanostructured gold surface. Analytical Chemistry 87:2588-2592.
  • Yuan T, Permentier H, Bischoff R. 2015. Surface-modified electrodes in the mimicry of oxidative drug metabolism. TrAC-Trends in Analytical Chemistry 70:50-57.

2014

  • Dashty M, Motazacker MM, Levels J, de Vries M, Mahmoudi M, Peppelenbosch MP, Rezaee F. 2014. Proteome of human plasma very low-density lipoprotein and low-density lipoprotein exhibits a link with coagulation and lipid metabolism. Thrombosis and Haemostasis 111(3):518-530.
  • Nadal-Jimenez P, Koch G, Reis CR, Muntendam R, Raj H, Jeronimus-Stratingh CM, Cool RH, Quax WJ. 2014. PvdP is a tyrosinase that drives maturation of the pyoverdine chromophore in Pseudomonas aeruginosa. Journal of Bacteriology 196(14):2681–2690.
  • Natalia D, Vidilaseris K, Ismaya WT, Puspasari F, Prawira I, Hasan K, Permentier HP, Nurachman Z, Subroto T, Dijkstra BW, Soemitro S. 2014. Effect of introducing a disulphide bond between the A and C domains on the activity and stability of Saccharomycopsis fibuligera R64 α-amylase. Journal of Biotechnology 195:8-14.
  • Ourailidou ME, van der Meer JY, Baas BJ, Jeronimus-Stratingh M, Gottumukkala AL, Poelarends GJ, Minnaard AJ, Dekker FJ. 2014. Aqueous oxidative Heck reaction as a protein-labeling strategy. ChemBioChem 15(2):209-212.
  • Sakulkhu U, Maurizi L, Mahmoudi M, Motazacker M, de Vries M, Gramoun A, Ollivier Beuzelin MG, Vallée JP, Rezaee F, Hofmann H. 2014. Ex situ evaluation of the composition of protein corona of intravenously injected superparamagnetic nanoparticles in rats. Nanoscale 6:11439-11450.
  • Salentijn GIJ, Permentier HP, Verpoorte E. 2014. 3D-printed paper spray ionization cartridge with fast wetting and continuous solvent supply features. Analytical Chemistry 86(23):11657-11665.
  • Siegel D, Meinema AC, Permentier H, Hopfgartner G, Bischoff R. 2014. Integrated quantification and identification of aldehydes and ketones in biological samples. Analytical Chemistry 86(10):5089-5100.
  • Siegel D, Permentier H, Reijngoud DJ, Bischoff R. 2014. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. Journal of Chromatography B 966:21-33.

2013

  • Avanti C, Hinrichs WLJ, Casini A, Eissens AC, van Dam A, Kedrov A, Driessen AJM, Frijlink HW, Permentier HP. 2013. The formation of oxytocin dimers is suppressed by the zinc-aspartate-oxytocin complex. Journal of Pharmaceutical Sciences 102(6):1734-1741.
  • Bouma HR, Mandl JN, Strijkstra AM, Boerema AS, Kok JW, van Dam A, IJzerman A, Kroese FG, Henning RH. 2013. 5'-AMP impacts lymphocyte recirculation through activation of A2B receptors. Journal of Leukocyte Biology 94(1):89-98.
  • Budnik LT, Preisser AM, Permentier H, Baur X. 2013. Is specific IgE antibody analysis feasible for the diagnosis of methylenediphenyl diisocyanate-induced occupational asthma? International Archives of Occupational and Environmental Health 86(4):417-430.
  • Happyana N, Agnolet S, Muntendam R, van Dam A, Schneider B, Kayser O. 2013. Analysis of cannabinoids in laser-microdissected trichomes of medicinal Cannabis sativa using LCMS and cryogenic NMR. Phytochemistry 87:51–59.
  • Meszaros P, Klappe K, van Dam A, Ivanovac PT, Milnec SB, Myers DS, Brown HA, Permentier H, Hoekstra D, Kok JW. 2013. Long term myriocin treatment increases MRP1 transport activity. The International Journal of Biochemistry & Cell Biology 45(2):326-334.
  • Roeser J, Alting NFA, Permentier HP, Bruins AP, Bischoff R. 2013. Chemical labeling of electrochemically cleaved peptides. Rapid Communications in Mass Spectrometry 27: 546-552.
  • Roeser J, Alting NFA, Permentier HP, Bruins AP, Bischoff R. 2013. Boron-doped diamond electrodes for the electrochemical oxidation & cleavage of peptides. Analytical Chemistry 85(14): 6626-6632.
  • Siegel D, Permentier H, Bischoff R. 2013. Controlling detrimental effects of metal cations in the quantification of energy metabolites via ultrahigh pressure-liquid chromatography-electrospray-tandem mass spectrometry by employing acetylacetone as a volatile eluent modifier. Journal of Chromatography A 1294:87–97.
  • Siissalo S, de Waard H, de Jager MH, Hayeshi R, Frijlink HW, Hinrichs WL, Dinter-Heidorn H, van Dam A, Proost JH, Groothuis GM, de Graaf IA. 2013. Nanoparticle formulation of a poorly soluble cannabinoid receptor 1 antagonist improves absorption by rat and human intestine. Drug Metabolism and Disposition 41:1557-1565.

2012

  • Avanti C, Permentier HP, van Dam A, Poole P, Jiskoot W, Frijlink HW, Hinrichs WLJ. 2012. A new strategy to stabilize oxytocin in aqueous solutions: II. Suppression of cysteine-mediated intermolecular reactions by a combination of divalent metal ions and citrate. Molecular Pharmaceutics 9(3):554-562.
  • Gandhi T, Puri P, Fusetti F, Breitling R, Poolman B, Permentier HP. 2012. Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS. Journal Proteome Research 11(8):4044-4051.
  • Nouri-Nigjeh E, Bruins AP, Bischoff R, Permentier HP. 2012. Electrocatalytic oxidation of hydrogen peroxide on a platinum electrode in the imitation of oxidative drug metabolism by Cytochrome P450s. Analyst 137:4698-4702.
  • Nouri-Nigjeh E, de Vries MP, Bruins AP, Bischoff R, Permentier HP. 2012. Electrochemical oxidation of quaternary ammonium electrolytes: unexpected side reactions in organic electrochemistry. Electrochemistry Communications 21:54-57.

2011

  • Bouma HR, Kroese FGM, Kok JW, Talaei F, Boerema AS, Herwig A, Draghiciu O, van Buiten A, Epema AH, van Dam A, Strijkstra AM Henning RH. 2011. Low body temperature governs the decline of circulating lymphocytes during hibernation through sphingosine-1-phosphate. Proceedings of the National Academy of Sciences 108(5):2052-2057.
  • Hendrawati O, Woerdenbag HJ, Michiels PJA, Aantjes HG, van Dam A, Kayser O. 2011. Identification of lignans and related compounds in Anthriscus sylvestris by LC-ESI-MS/MS and LC-SPE-NMR. Phytochemistry 72(17):2172-2179.
  • Klepsch MM, Kovermann M, Löw C, Balbach J, Permentier HP, Fusetti F, de Gier JW, Slotboom DJ, Berntsson RPA. 2011. Escherichia coli peptide binding protein OppA has a preference for positively charged peptides. Journal of Molecular Biology 414(1):75-85.
  • Marreddy RKR, Pinto JPC, Wolters JC, Geertsma ER, Fusetti F, Permentier HP, Kuipers OP, Kok J, Poolman B. 2011. The response of Lactococcus lactis to membrane protein production. Plos One 6(8).
  • Natalia D, Vidilaseris K, Satrimafitrah P, Purkan WTI, Permentier H, Fibriansah G, Puspasari F, Nurachman Z, Dijkstra BW, Soemitro S. 2011. Biochemical characterization of a glucoamylase from Saccharomycopsis fibuligera R64. Biologia 66(1):27-32.
  • Nouri-Nigjeh E, Bischoff R, Bruins AP, Permentier HP. 2011. Electrochemistry in the mimicry of oxidative drug metabolism by cytochrome P450s. Current Drug Metabolism 12(4):359-371.
  • Nouri-Nigjeh E, Bischoff R, Bruins AP, Permentier HP. 2011. Electrochemical oxidation by square-wave potential pulses in the imitation of phenacetin to acetaminophen biotransformation. Analyst 136(23):5064-5067.
  • Nouri-Nigjeh E, Permentier HP, Bischoff R, Bruins AP. 2011. Electrochemical oxidation by square-wave potential pulses in the imitation of oxidative drug metabolism. Analytical Chemistry 83(14):5519-5525.

2010

  • Gandhi T, Fusetti F, Wiederhold E, Breitling R, Poolman B, Permentier HP. 2010. Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples. Journal of Proteome Research 9(11):5922-5928.
  • Klappe K, Dijkhuis AJ, Hummel I, van Dam A, Ivanova PT, Milne SB, Myers DS, Brown HA, Permentier H, Kok JW. 2010. Extensive sphingolipid depletion does not affect lipid raft integrity or lipid raft localization and efflux function of the ABC transporter MRP1. Biochemical Journal 430:519-529.
  • Marreddy RKR, Geertsma ER, Permentier HP, Pinto JPC, Kok J, Poolman B. 2010. Amino acid accumulation limits the overexpression of proteins in Lactococcus lactis. Plos One 5(4).
  • Nouri-Nigjeh E, Permentier HP, Bischoff R, Bruins AP. 2010. Lidocaine oxidation by electrogenerated reactive oxygen species in the light of oxidative drug metabolism. Analytical Chemistry 82(18):7625-7633.
  • Roeser J, Bischoff R, Bruins AP, Permentier HP. 2010. Oxidative protein labeling in mass-spectrometry-based proteomics. Analytical and Bioanalytical Chemistry 397(8):3441-3455.
  • Roeser J, Permentier HP, Bruins AP, Bischoff R. 2010. Electrochemical oxidation and cleavage of tyrosine- and tryptophan-containing tripeptides. Analytical Chemistry 82(18):7556-7565.
  • de Vries L, Reitzema-Klein C, Meter-Arkema A, van Dam A, Rink R, Moll GN, Akanbi MHJ. 2010. Oral and pulmonary delivery of thioether-bridged angiotensin-(1-7). Peptides 31(5):893-898.

Before 2010

  • Guo XH, Bruins AP, Covey TR, Trötzmüller M, Lankmayr E. 2009. Alternative reagents for chemical noise reduction in liquid chromatography-mass spectrometry using selective ion-molecule reactions. Journal of the American Society for Mass Spectrometry 20(1):105-111.
  • Wiederhold E, Gandhi T, Permentier HP, Breitling R, Poolman B, Slotboom DJ. 2009. The yeast vacuolar membrane proteome. Molecular & Cellular Proteomics 8(2):380-392.
  • El Khattabi M, van Roosmalen ML, Jager D, Metselaar H, Permentier H, Leenhouts K, Broos J. 2008. Lactococcus lactis as expression host for the biosynthetic incorporation of tryptophan analogues into recombinant proteins. Biochemical Journal 409:193-198.
  • van Loo B, Permentier HP, Kingma J, Baldascini H, Janssen DB. 2008. Inactivation of epoxide hydrolase by catalysis-induced formation of isoaspartate. FEBS Letters 582(11):1581-1586.
  • Permentier HP, Bruins AP, Bischoff R. 2008. Electrochemistry-mass spectrometry in drug metabolism and protein research. Mini-Reviews in Medicinal Chemistry 8(1):46-56.
  • Windt W, van Dokkum RPE, Kluppel CA, Jeronimus-Stratingh CM, Hut F, de Zeeuw D, Henning RH. 2008. Therapeutic resistance to angiotensin converting enzyme (ACE) inhibition is related to pharmacodynamic and -kinetic factors in 5/6 nephrectomized rats. European Journal of Pharmacology 580(1-2):231-240.
  • Duurkens RH, Tol MB, Geertsma ER, Permentier HP, Slotboom DJ. 2007. Flavin binding to the high affinity riboflavin transporter RibU. Journal of Biological Chemistry 282(14):10380-10386.
  • Gosiewska S, Permentier HP, Bruins AP, van Koten G, Klein Gebbink RJM. 2007. Characterization and alkane oxidation activity of a diastereopure seven-coordinate iron(III) alkylperoxo complex. Dalton Transactions 31:3365-3368.
  • Guo XH, Bruins AP, Covey TR. 2007. Method to reduce chemical background interference in atmospheric pressure ionization liquid chromatography-mass spectrometry using exclusive reactions with the chemical reagent dimethyl disulfide. Analytical Chemistry 79(11):4013-4021.
  • de Jong LAA, Jeronimus-Stratingh CM, Cremers TIFH. 2007. Development of a multiplex non-radioactive receptor assay: The benzodiazepine receptor, the serotonin transporter and the beta-adrenergic receptor. Rapid Communications in Mass Spectrometry 21(4):567–572.
  • Bambirra S, Meetsma A, Hessen B, Bruins AP. 2006. Cationic group 3 alkyl complexes with isopropyl-substituted triazacyclononane-amide ligands: Synthesis, structure, and thermal decomposition processes. Organometallics 25:3486-3495.
  • Guo XH, Bruins AP, Covey TR. 2006. Characterization of typical chemical background interferences in atmospheric pressure ionization liquid chromatography-mass spectrometry. Rapid Communications in Mass Spectrometry 20(20):3145-3150.
  • Kauppila TJ, Bruins AP, Kostiainen R. 2005. Effect of the solvent flow rate on the ionization efficiency in atmospheric pressure photoionization-mass spectrometry. Journal of the American Society for Mass Spectrometry 16(8):1399-1407.
  • Panella L, Broos J, Jin JF, Fraaije MW, Janssen DB, Jeronimus-Stratingh M, Feringa BL, Minnaard AJ, de Vries JG. 2005. Merging homogeneous catalysis with biocatalysis; papain as hydrogenation catalyst. Chemical Communications (45):5656-5658.
  • Kauppila TJ, Kostiainen R, Bruins AP. 2004. Anisole, a new dopant for atmospheric pressure photoionization mass spectrometry of low proton affinity, low ionization energy compounds. Rapid Communications in Mass Spectrometry 18(7):808-815.
  • Kauppila TJ, Kotiaho T, Kostiainen R, Bruins AP. 2004. Negative ion-atmospheric pressure photoionization-mass spectrometry. Journal of the American Society for Mass Spectrometry 15(2):203-211.
  • Permentier HP, Bruins AP. 2004. Electrochemical oxidation and cleavage of proteins with on-line mass spectrometric detection: Development of an instrumental alternative to enzymatic protein digestion. Journal of the American Society for Mass Spectrometry 15(12):1707-1716.
  • Wang X, Permentier HP, Rink R, Kruijtzer JAW, Liskamp RMJ, Wösten HAB, Poolman B, Robillard GT. 2004. Probing the self-assembly and the accompanying structural changes of hydrophobin SC3 on a hydrophobic surface by mass spectrometry. Biophysical Journal 87(3):1919-1928.
  • van Hout MWJ, Hofland CM, Niederländer HAG, Bruins AP, de Zeeuw RA, de Jong GJ. 2003. On-line coupling of solid-phase extraction with mass spectrometry for the analysis of biological samples: III. Determination of prednisolone in serum. Journal of Chromatography B 794(1):185-192.
  • Jurva U, Wikström HV, Weidolf L, Bruins AP. 2003. Comparison between electrochemistry/mass spectrometry and cytochrome P450 catalyzed oxidation reactions. Rapid Communications in Mass Spectrometry 17(8):800-810.
  • Permentier HP, Jurva U, Barroso B, Bruins AP. 2003. Electrochemical oxidation and cleavage of peptides analyzed with on-line mass spectrometric detection. Rapid Communications in Mass Spectrometry 17(14):1585-1592.
  • Jurva U, Wikström HV, Bruins AP. 2002. Electrochemically assisted Fenton reaction: Reaction of hydroxyl radicals with xenobiotics followed by on-line analysis with high-performance liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry 16(20):1934-1940.
  • Polderman-Tijmes JJ, Jekel PA, Jeronimus-Stratingh CM, Bruins AP, van der Laan JM, Sonke T, Janssen DB. 2002. Identification of the catalytic residues of alpha-amino acid ester hydrolase from Acetobacter turbidans by labeling and site-directed mutagenesis. Journal of Biological Chemistry 277(32):28474-28482.
  • Jurva U, Wikström HV, Bruins AP. 2000. In vitro mimicry of metabolic oxidation reactions by electrochemistry/mass spectrometry. Rapid Communications in Mass Spectrometry 14(6):529-533.
  • Robb DB, Covey TR, Bruins AP. 2000. Atmospheric pressure photoionisation: An ionization method for liquid chromatography-mass spectrometry. Analytical Chemistry 72(15):3653-3659.
  • Bruins CHP, Jeronimus-Stratingh CM, Ensing K, van Dongen WD, de Jong GJ. 1999. On-line coupling of solid-phase extraction with mass spectrometry for the analysis of biological samples: I. Determination of clenbuterol in urine. Journal of Chromatography A 863(1):115-122.
  • Bruins AP. 1998. Mechanistic aspects of electrospray ionization. Journal of Chromatography A 794(1-2):345-357.
  • Kunji ERS, Fang G, Jeronimus-Stratingh CM, Bruins AP, Poolman B, Konings WN. 1998. Reconstruction of the proteolytic pathway for use of beta-casein by Lactococcus lactis. Molecular Microbiology 27(6):1107-1118.
  • van der Wal S, Mengerink Y, Brackman JC, de Brabander, EMM, Jeronimus-Stratingh CM, Bruins AP. 1998. Compositional analysis of nitrile terminated poly(propylene imine) dendrimers by high-performance liquid chromatography combined with electrospray mass spectrometry. Journal of Chromatography A 825(2):135-147.


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