Analytical Biochemistry, Annual Report 2013

faculty of mathematics
and natural sciences
department of pharmacy
Analytical Biochemistry
Annual Report 2013
Prof.Dr. Rainer Bischoff
15 January 2014
Analytical Biochemistry › 2
Group Photo Analytical Biochemistry & Mass Spectrometry Center
Back row: Kees Bronsema, Turan Gül, Daniël Wilffert, Peter Horvatovich, Nico van de
Merbel, Alexander Boychenko, Tao (Larry) Zhang, Natalia Govorukhina, Hjalmar
Permentier, Sara Ongay Camacho, Marcel de Vries, Amanda Lucas, Mikhael Sowma,
Hong Yumiao, Frank Schalk
Front Row: Jos Hermans, Jan Willem Meints, Jolanda Meindertsma, Rainer
Bischoff, Margot Jeronimus-Stratingh, Karin Wolters, Tao Yuan, Yun Yang
Not on photo: David Siegel, Annie van Dam
Address:
University of Groningen
Department of Pharmacy
Analytical Biochemistry
Antonius Deusinglaan 1
Postbus 196
9700 AD Groningen
The Netherlands
Head of the research group:
Prof. Dr. Rainer Bischoff
Phone: (+31)-50-363-3338
Fax: (+31)-50-363-7582
E-mail: [email protected]
Website: www.biomac.nl
Analytical Biochemistry › 3
Members of the Research Group:
Staff
Prof. Dr. Rainer Bischoff
Prof. Dr. Peter Horvatovich
Prof. Dr. Nico van de Merbel (professor through special appointment)
Dr. Natalia Govorukhina
Jos Hermans
Jan Willem Meints
Jolanda Meindertsma (secretary; 0.4 fte)
Mass Spectrometry Centre
Dr. Hjalmar Permentier
Annie van Dam (0.5 fte)
Margot Jeronimus-Stratingh (0.5 fte)
Post-doctoral researchers
Dr. Alexander Boychenko
Dr. Sara Ongay Camacho
Dr. Karin Wolters (until June 30, 2013)
Dr. David Siegel
Ph.D. students
Kees Bronsema
Lorenza Franciosi
Berend Hoekman (group Horvatovich)
Vikram Mitra (group Horvatovich)
Daniël Wilffert
Yun Yang
Turan Gül
Tao Yuan
Tao (Larry) Zhang
Research Students
Georgia Koutsoumpli, Topmaster MPDI
Niels Alting, Master Medical Pharmaceutical Sciences
Jennifer Schlaman, Bachelor Hanzehogeschool
Nadjib Bawary, Master Pharmacy
Amanda Lucas, Master Pharmacy
Frank Schalk, Bachelor Hanzehogeschool
Hong Yumiao, Master Medical Pharmaceutical Sciences
Visiting scientists and students
Miina Ruokolainen, PhD student, University of Helsinki, Finland, May 2013, EC-MS of
drug compounds: “Imitation of phase I metabolism reactions by photocatalysis and
electrochemical reactions”.
Kundai Sachikonye, Jacobs University Bremen, Germany. June 2013, Summer
internship student project: Project: “Discovery and validation of protein biomarkers for
cervical cancer”.
Analytical Biochemistry › 4
Overview 2013
A major highlight of the year 2013 was the promotion of Peter Horvatovich to
associate professor in Computational Mass Spectrometry with tenure in June. Peter has
been with the group since he started his postdoctoral studies in 2005. As postdoctoral
researcher and as assistant professor during his tenure-track, Peter contributed
significantly to the development of bioinformatics procedures in the group notably the
processing of LC-MS/MS data. Peter built an international reputation over the years for
himself and the group in this field, which has recently been acknowledged by his
nomination to join the editorial advisory board of the Journal of Proteome Research
one of the leading proteomics journals published by the American Chemical Society. I
wish Peter success in his future career and welcome him as a colleague in the research
group.
Another major event in 2013 was moving from our old location in building 3211 to
the new European Research Institute for the Biology of Ageing (ERIBA). By moving the
Analytical Biochemistry group we also joined hands with the colleagues from the Mass
Spectrometry Center. The move went rather smoothly thanks to the diligent and
detailed preparations made notably by Hjalmar Permentier (head of the MS Center)
and Jos Hermans. Although we had to move 16 LC-MS systems, about everything was
up and running again within 1-2 weeks after the move. Despite some initial scepticism,
we quickly started to realize how much we have gained by moving both groups together
and by the more intense interaction with colleagues from the science and the medical
science faculties. Please take a look at the Annual Report of the MS Center @
www.biomac.nl.
During 2013 we also got together with old and new colleagues at the Department of
Pharmacy that focus on chemistry in the wider sense of the term to instil new life into
this research program of the Groningen University Research Institute of Drug
Exploration (GUIDE). Due to its wider scope, we renamed the program Medicinal
Chemistry and Bioanalysis (MCB, see the MCB flyer @ www.biomac.nl)). To inaugurate
the program as well as the new laboratory @ ERIBA, we will hold a symposium on
August 25-26, 2014 in Groningen and start with a regular program of research
presentations and discussions. It’s great to be working in such a stimulating
atmosphere!
The end of the year 2013 brought 2 successful grant applications, one by Nico van de
Merbel in the area of Biopharmaceuticals and one in the area of Biomarkers. Notably
the large program grant from the Dutch Technology Foundation to establish a
Biomarker Development Center (BDC) in the Netherlands in collaboration with
colleagues from the University Medical Centres in Nijmegen and Rotterdam is a big
step forward. It will foster national and international collaborations and bring
sustainability to this research line.
It is not possible to mention everything that has happened in this very busy year but
the finalization of the PhD theses of Julien Roeser and Laurette Prély should not go
unmentioned. The continued hard work of especially the staff members of the group to
educate the next generation of scientists through a range of courses (see page 27 for an
overview) was again a major contribution in 2013. My thanks to everyone who made
this possible.
I wish you interesting reading of this Annual Report and a successful year 2014. In
case you see possibilities for future collaborations, I would be happy to discuss them
with you.
Analytical Biochemistry › 5
Research Projects
1. Cervical Cancer Biomarkers
The cervical cancer project is run in collaboration with the groups of Ate van der Zee
(UMCG) and Theo Luider (Erasmus University Medical Center, Rotterdam). Coworkers
that are actively involved in this project are Natalia Govorukhina and Alexander
Boychenko in Groningen and Coskun Güzel in Rotterdam. The project is funded by the
Dutch Cancer Society (KWF).
Project Description
Cervical carcinoma is the second most frequent carcinoma in women worldwide,
while in the developing countries cervical carcinoma is the most frequent carcinoma in
women. In this project, we are developing new approaches based on LC-MS/MS to
detect biomarkers for the early diagnosis and prognosis of cervical cancer based on
serum and tissue analyses.
Current work focuses on validating biomarker candidates that were discovered by
targeted tissue analysis after laser-guided microdissection or through serum analysis.
To this end colleagues in Rotterdam developed a 2-dimensional nanoLC-MS/MS
method to measure HSP-90 in serum at the ng/mL level without the use of antibodies.
After confirming the initially discovered serum biomarker candidates, the Groningen
team developed a quantitative LC-MS/MS method in the SRM mode and is currently in
the middle of a large verification study comparing healthy controls, with patients with
precancerous lesions (CIN) and patients with early- and late-stage cervical carcinoma.
Notably the differentiation of patients with CIN lesions that may or may not develop
into cancer from healthy controls is challenging but initial data are encouraging (see
figure below).
ROC curve for discriminating patients
with precancerous CIN lesions from
healthy subjects based on the
measurement of multiple serum
proteins by LC-MS/MS (SRM mode)
Area under the ROC curve 0.85.
Next to validating biomarker candidates in a larger set of serum samples, we have
initiated another round of discovery work based on laser-guided microdissection of
tissue from cancer patients and controls as well as on a more in-depth serum analysis
by depleting 64 proteins using immunoaffinity chromatography. To enhance proteome
coverage we have developed better sample preparation and separation methods at the
peptide level using 2- and 3-dimensional LC.
Analytical Biochemistry › 6
2. Data processing and statistical analysis (group Horvatovich)
This research line has been carried out by two PhD students Vikram Mitra and
Berend Hoekman under the supervision of Peter Horvatovich. It is expected that
Vikram Mitra and Berend Hoekman will defend their theses in 2014. The fruitful
collaboration with Frank Suits from IBM and the group of Gyorgy Marko-Varga at
Lund University (Sweden) continued and resulted in two publications on a data preprocessing pipeline for MALDI imaging analysis. Collaboration with the Laboratoire de
Chimie Analytique et Sciences de l’Aliment (Strasbourg, France) resulted in a
publication on the topic of biomarker discovery to identify Lactic bacilli with probiotic
properties. Peter Horvatovich was invited to edit a book on “Comprehensive Biomarker
Discovery and Validation for Clinical Application” published by the Royal Chemistry
Society (UK) with Rainer Bischoff as co-editor. Peter Horvatovich is further actively
involved as member of the Chromosome 5 team of the Chromosome Centric Human
Proteome Project, an initiative of the Human Proteome Organization (HUPO). Further
research lines that are currently pending to receive funding are the development of a
bioinformatics platform for the detection of low abundant peptides and proteins and to
the development of a novel sensitive targeted Mass Spectrometry Imaging approach
using photo-cleavable mass tags (collaboration with Angela Casini).
Project Description
The analysis of complex mixtures with hyphenated analytical methods like LCMS/MS generates enormous amounts of data corresponding to several tens of
thousands of compounds (variables) per sample. In order to be able to compare a
limited number of samples in typical biomarker discovery projects, it is thus vital to
reduce the number of variables without losing relevant information. The way from the
raw data to the so-called “clean data” is denominated as data pre-processing.
Development of efficient and reliable data pre-processing algorithms requires
knowledge of both the mathematical background of the data processing steps as well as
a good understanding of the structure of the data and the analytical procedures through
which artefacts may have been generated.
The work of Christin on the comparative evaluation of six different statistical
approaches for biomarker discovery (published in Molecular & Cellular Proteomics)
was performed in close collaboration with colleagues at the University of Amsterdam
(Age Smilde, Huub Hoefsloot). Berend Hoekman finalized the extension of the
msCompare framework for quantitative pre-processing of label-free 2-dimensional LCMS/MS data and finalized the development of a liquid chromatography gradient
optimization method to improve the identification efficiency within a given LC-MS/MS
analysis of complex proteomics samples.
Analytical Biochemistry › 7
Overview of the two best performing feature selection statistical methods for two differentially
spiked LC-MS data sets (first dataset: 0a, 0b; second dataset: 1a-c, 2a-c) of different sample
size and extent of between- and within-class variability (from Christin et al., Mol. Cell. Prot. 12
(2013) 263-276).
Though Ishtiaq Ahmad is now working at the University of Amsterdam, we are still
collaborating on the implementation of a comprehensive complete data (pre)processing pipeline starting from raw mass spectrometry data all the way to knowledge
discovery on the NBIC Galaxy server (http://galaxy.nbic.nl/) in collaboration with
several Dutch research groups.
Vikram Mitra finalized his project to develop a quality control method, which
assesses whether it is possible to align all peaks in two chromatograms with the same
accuracy (paper under review at the J. Proteome Res.). The second manuscript, which
describes a statistical approach to analyse data sets obtained in an experimental design
study, is at the final stage. This work has the goal to assess the importance of preanalytical factors affecting the quantitative molecular profile of complex shotgun
proteomics samples. The work is performed in close collaboration with our colleagues
at the University of Amsterdam (Age Smilde, Gooitzen Zwanenburg). Vikram is also at
an advanced stage with his third manuscript on identification transfer between
complex LC-MS(/MS) data sets despite the fact that he started his new job at Proteome
Sciences plc (London, UK) on April 01, 2013.
Analytical Biochemistry › 8
3. Electrochemistry
The different lines of this project are run in collaboration between the Analytical
Biochemistry
group
&
the
Mass
Spectrometry
Center
with
the
Biochemistry/Biotechnology group at the University of Groningen (Marco Fraaije) and
the BIOS - lab on a chip group at the University of Twente (Albert van den Berg,
Wouter Olthuis and Matthieu Odijk). Work on the electrochemical cleavage of peptides
and proteins (Larry Zhang) made progress by performing the subsequent coupling
reaction of the spirolactone-containing cleavage product in an organic solvent. The
semi-preparative electrochemical synthesis of Phase-I drug metabolites (Turan Gül)
has advanced thanks to a systematic optimization using a Design-of-Experiment (DoE)
approach and the recent implementation of up-scale equipment. The surface
modification of electrodes (Tao Yuan) is currently being studied in detail using surfaceenhanced Raman spectroscopy (SERS) in close collaboration with colleagues from the
University of Twente. The immobilization of FAD-dependent monooxygenases
(Marzena Krzek, group Fraaije) was successful using agarose beads and we are eagerly
awaiting results whether this enzyme can be functionally coupled to a surface-modified
electrode.
The project lines are funded by the Dutch Technology Foundation (STW), the Dutch
Research Organization (NWO, ECHO grant, collaboration Fraaije) and the Chinese
Scholarship Council (CSC, Larry Zhang).
Project Description
The projects aim at a) the electrochemical cleavage of peptides and proteins, b) the
semi-preparative electrochemical synthesis of Phase-I drug metabolites, c) the surface
modification of electrodes and d) the immobilization of FAD-dependent
monooxygenases. Output from earlier work has resulted in 2 publications in 2013 in the
field of peptide cleavage and capture.
Scale-up of the generation of the N-dealkylation product of lidocaine using a preparative
electrochemical batch cell (n=2).
Analytical Biochemistry › 9
4. Electrospray Ionization Response
This work is performed by Jos Hermans and Sara Ongay Camacho. In this project
we study the effect of different chemical derivatization reagents on the electrospray
ionization response of low-molecular weight analytes in relation to their physicochemical properties.
Project Description
Many low-molecular weight hydrophilic compounds are not amenable to highsensitivity LC-MS analysis using electrospray ionization (ESI). Furthermore, these
compounds are often not retained on reversed-phase chromatographic stationary
phases and thus escape detection altogether. Earlier work showed that the ionization
efficiency of amino acids upon ESI can be markedly enhanced by coupling
polyethyleneglycol derivatives to these compounds (Abello et al., Anal. Chem., 2008,
80: 9171).
In this project we investigate potential mechanisms underlying this enhancement by
correlating the ESI signals of various amino acid derivatives with calculated physicochemical properties. While there is a clear correlation between the molecular volume
and the ESI response for amino acids that are derivatized with aliphatic organic acids,
this is not the case for PEG-derivatization (see below). This project will be continued by
studying other relationships.
Correlation between the
calculated molecular
volume and the
electrospray ionization
response of derivatized
amino acids using a flowinjection system. PEG
(polyethyleneglycol); BU
(butyl); PR (propyl); AC
(acetyl); AA-FIA (nonderivatized amino acids)
Analytical Biochemistry › 10
5. Protein analysis for systems biology
As part of the Systems Biology Center for Energy Metabolism and Ageing Research
(SBC-EMA) Karin Wolters (postdoctoral researcher) established quantitative protein
analysis methodology based on protein-specific peptides by LC-MS/MS in the selected
reaction monitoring (SRM) mode. We currently apply these methods to ageing yeast
cells (coll. Matthias Heinemann) and mouse models (coll. Barbara Bakker) under
different conditions of energy usage and physical activity. Data provided to the
colleagues focusing on yeast cells are currently being analysed and integrated into
systems biology models.
Project Description
Development of targeted proteomics assays for yeast
For the assay development of yeast target proteins, isotopically labelled cells
(metabolic labelling) were grown under various conditions to achieve maximal coverage
for all target proteins. With these samples, assays were developed for proteins
belonging to energy metabolism pathways, the nuclear pore complex and other targets
related to ageing. Quantitative data has been acquired for the ageing related targets
using replicatively aged yeast cells (data acquisition finished; data analysis ongoing). In
parallel we are setting up assays to study the composition of the nuclear pore complex
(coll. Liesbeth Veenhoff) in yeast cells using the QConCat approach (coll. Rob Beynon,
University of Liverpool, UK) for absolute quantification.
Development of targeted proteomics assays for mouse
Protein extraction from various mouse tissues and organelles has been optimized
and absolute quantifications will be obtained using QConCATs specific for a subset of
proteins from the energy metabolic and the fatty acid β-oxidation pathways (in total 57
proteins). Targeted protein analyses from a test set of aged mice are ongoing.
Expanding the scope of targeted proteomics
Possibilities are currently explored to expand the scope of biological questions that
can be addressed using targeted proteomics. In one sub-project we study the
phosphorylation state of hexokinase 2 at two sites in relation to various glycolytic
fluxes in yeast cells (coll. Matthias Heinemann).
T (min)
0 2 5 10 15 20 30 60 90
1P
0P
Phosphorylation state of
hexokinase 2 in yeast.
Upper part: total phosphorylation
state determined with a phostag
gel (courtesy Guille Zampar).
Lower part: total phosphorylation
state quantified from the phostag
gel (in red) and through
quantification of one
phosphorylation site by LC-MS/MS
(in black). Note the generally
better precision of the MS
analysis.
Analytical Biochemistry › 11
6. Metabolite analysis for systems biology
David Siegel (postdoctoral fellow) developed LC-MS/MS methodology to quantify
the main metabolites involved in cellular energy metabolism based on LC-MS/MS in
the SRM mode. We are currently able to quantify some 70 metabolites using a 13Clabelled global internal standard obtained from yeast cultures grown on 13C-glucose.
A number of issues associated with the quantification of highly polar small
molecules were investigated as well. For instance, we studied the effect of metal ions in
the LC mobile phase on sensitivity and other analytical figures of merit. Eluent
modification with a volatile metal chelator was found to resolve related issues and
improved almost all analytical performance parameters in typical targeted analyses.
Representation of the effect of eluent modification with a volatile metal chelator (acetylacetone)
on UHPLC-ESI(-)-MS/MS peak properties. The chromatograms shown are technical replicates
with increasing concentrations of acetylacetone in the UHPLC eluent (CoA = Coenzyme A)
(from Siegel et al., J. Chrom. A., 2013, 1294: 87).
A general review of analytical issues in energy metabolite quantification was
furthermore published and forms the basis for a PhD project starting in February 2014.
In the frame of this project we will systematically study chemical degradation of
different classes of metabolites during the pre-analytical phase and develop approaches
to address such issues wherever feasible.
Analytical Biochemistry › 12
7. LC-MS/MS analysis of protein pharmaceuticals in complex
biological matrices
This project is part of a collaboration with the Pharmaceutical Biology group at the
University of Groningen (Wim Quax), with Utrecht University (Ad de Jong) and the
Free University of Amsterdam (Wilfried Niessen, Govert Somsen), the Bioanalytical
Laboratory at PRA (Nico van de Merbel), and a number of industrial partners funded
by the Dutch Technology Foundation (STW). In 2013 we focused on different aspects of
the analysis of protein biopharmaceuticals related to protein and peptide enrichment
without antibodies and the systematic evaluation of the effect of internal standards on
method performance.
Major achievements in 2013 were the high-sensitivity analysis of salmon calcitonine
in human plasma at 10 pg/mL and the analysis of TRAIL (wild-type and one sitedirected variant) in human and mouse serum at 20 ng/mL. Both methods were fully
validated according to international guidelines for the bioanalysis of pharmaceuticals
(e.g. as stipulated by the FDA).
Project Description
Protein pharmaceuticals or “biopharmaceuticals” form a class of innovative
therapeutic agents that are rapidly increasing in relevance for health care. In order to
develop these macromolecules into effective and safe products it is necessary to dispose
of analytical methods that can characterize them at the molecular level and that allow
to follow them in vivo during clinical development and in clinical practice.
In a consortium between leading academic groups in analytical chemistry in the
Netherlands, instrument manufacturers and pharmaceutical companies we develop
highly sensitive and selective methods for biopharmaceutical analysis. In Groningen,
Daniël Wilffert (PhD student), Carlos Reis and Ingrid van Roosmalen (group of Wim
Quax) study variants of TRAIL in body fluids and cell culture by LC-MS/MS. The first
method for serum analysis has been validated and successfully applied to an in vivo
pharmacokinetic study in mice. This method reaches low ng/mL sensitivity without the
use of antibodies and allows the simultaneous quantification of TRAIL wild-type and
one variant.
The project of PhD student Kees Bronsema focuses on the ultra-sensitive,
quantitative analysis of peptide pharmaceuticals and biomarkers by LC-MS/MS in the
SRM mode. Next to the low pg/mL quantification of the peptide salmon calcitonine, the
antibody-free analysis of single-chain antibodies (so-called nanobodies) has been
successfully completed down to the low ng/mL level. We have recently extended these
analyses to enzymes that are used in replacement therapy and to monoclonal
antibodies in collaboration with the Hospital Pharmacy Department of the University
Medical Center Groningen (Daan Touw).
LC-MS/MS of salmon calcitonine in human plasma at 10 pg/mL (from Bronsema et al., Anal.
Chem., 2013, 85: 9528).
Analytical Biochemistry › 13
8. Development of reversible crosslinkers for histochemistry and
proteomics
In this project we develop and evaluate reversible chemical crosslinkers that can be
cleaved under specified conditions in collaboration with the Pharmacokinetics,
Toxicology and Targeting group at the University of Groningen (Geny Groothuis) and a
number of collaborating groups in an NWO-funded project as part of the COAST
program. Based on progress with the chemical synthesis (Leiden University, group of
Hermen Overkleeft) we hope to extend this principle to crosslinkers with added
functionalities, for example for easier protein quantification or enrichment. Our initial
results show that a reversible crosslinker which can be cleaved with periodate allows
recovering more protein from paraffin-embedded fixated tissue. Further proteomics
analyses will show whether this translates into more identified proteins.
Project Description
Histochemistry (HC) is widely used in pathology to diagnose disease, to
prognosticate disease development and to stratify patients for subsequent therapeutic
interventions.
Histochemistry
combined
with
immunological
detection
(immunohistochemistry or IHC) is a very important technique in clinical research. HC
is based on fixating tissue by protein crosslinking using paraformaldehyde followed by
embedding in paraffin. While this allows the detailed microscopic analysis of tissue
sections as well as their conservation over extended periods of time at room
temperature, it is currently very difficult to perform comparative quantitative protein
analyses on fixated and paraffin embedded tissue due to crosslinks between proteins.
In an effort to combine tissue fixation with subsequent proteomic analysis, for example
after laser-guided microdissection, we initiated a collaborative project between
academic groups and industry on novel chemical crosslinkers with added functionality
funded by the NWO-ACTS program (sub-program COAST).
SDS-PAGE analysis of crosslinked lysozyme as
surrogate for fixated tissue. A) prior to cleavage with
periodate and B) after cleavage with periodate.
Analytical Biochemistry › 14
Ph.D. projects:
B. Hoekman
Development of a comprehensive data processing and statistical analysis methodology
for label-free LC-MS data in biomarker discovery
Promotor: Prof. Dr. P.L. Horvatovich
Co-promotors: Prof. Dr. R. Bischoff, Prof. Dr. R. Breitling (University of Manchester)
Start: September 2007
L. Franciosi
Acute and chronic inflammatory responses induced by smoking in individuals being
susceptible and non-susceptible for development of COPD: from specific disease
phenotyping towards novel tailor-made therapy
Promotors: Prof. Dr. R. Bischoff, Prof. Dr. D.S. Postma (UMCG), Dr.
N.H.T. ten Hacken (UMCG)
Supervisor: Dr. N. Govorukhina
Start: February 2008
V. Mitra
Quantitation, processing and classification algorithms for mass spectrometry
Promotor: Prof. Dr. P.L. Horvatovich
Co-promotors: Prof. Dr. R. Bischoff, Prof. Dr. A.K. Smilde (University of Amsterdam)
Start: April 2009
K. Bronsema
Quantitative determination of biopharmaceuticals in biological fluids using LC-MS
based techniques
Promotors: Prof. Dr. N.C. van de Merbel, Prof. Dr. R. Bischoff
Start: September 2010
D. Wilffert
Analysis of Biopharmaceuticals by LC-MS/MS
Promotors: Prof. Dr. R. Bischoff, Prof. Dr. W.J. Quax, Prof. Dr. N.C. van
de Merbel
Supervisors: J. Hermans, Dr. N. Govorukhina
Start: August 2011
Y. Yang
Mixed mode chromatography in proteomic biomarker discovery: focus on
nitrotyrosine-modified proteins
Promotors: Prof. Dr. R. Bischoff, Prof. Dr. I. Kema (UMCG)
Supervisor: Dr. S. Ongay Camacho
Start: November 2011
T. Zhang
LC-Electrochemistry - Mass Spectrometry in Protein Chemistry
Promotors: Prof. Dr. R. Bischoff, Prof. Dr. I. Kema (UMCG)
Supervisor: Dr. H. Permentier
Start: September 2012
T. Gül
Electrochemistry – Mass Spectrometry (EC-MS) for Drug Metabolism
Promotor: Prof. Dr. R. Bischoff
Supervisor: Dr. H. Permentier
Start: September 2012
Analytical Biochemistry › 15
T. Yuan
Electrochemistry combined with mass spectrometry to study drug metabolism
Promotor: Prof. Dr. R. Bischoff
Supervisor: Dr. H. Permentier
Start: October 2012
Analytical Biochemistry › 16
Scientific Output 2013
Theses
Roeser, J., Electrochemical oxidation and cleavage of peptides in bioanalysis.
Mechanistic aspects & method development.
Promotor: Prof. Dr. R. Bischoff; co-promotors: Dr. A.P. Bruins, Dr. H.P. Permentier.
Dissertation University of Groningen, March 8, 2013, 159 pp.
Prely, L.M., Activity-based and targeted analyses of matrix-metalloproteases.
Promotors: Prof. Dr. R. Bischoff, Prof. Dr. A.J.M. van Oosterhout.
Dissertation University of Groningen, October 28, 2013, 108 pp.
Scientific publications
Peer-reviewed
Avanti, C., Hinrichs, W.L.J., Casini, A., Eissens, A.C., Dam, A. van, Kedrov, A.,
Driessen, A.J.M., Frijlink, H.W., Permentier, H.P., The formation of oxytocin dimers is
suppressed by the zinc-aspartate-oxytocin complex. J. Pharmacol. Sci. 102 (2013) 17341741
Bischoff, R., Bronsema, K.J., Merbel, N.C. van de, Analysis of biopharmaceutical
proteins in biological matrices by LC-MS/MS. I. Sample preparation. Trends Anal.
Chem. 48 (2013) 41-51
Boichenko, A., Govorukhina, N., Zee, A.G.J. van der, Bischoff, R., Simultaneous serum
desalting and total protein determination with macroporous reversed-phase
chromatography. Anal. Bioanal. Chem. 405 (2013) 3195-3203
Boichenko, A.P., Govorukhina, N., Zee, A.G.J. van der, Bischoff, R., Multidimensional
separation of tryptic peptides from human serum proteins using reversed-phase, strong
cation exchange, weak anion exchange, and fused-core fluorinated stationary phases. J.
Sep. Sci. 36 (2013) 3463-3470
Bouma, H.R., Mandl, J.N., Strijkstra, A.M., Boerema, A.S., Kok, J.W., Dam, A. van,
IJzerman, A., Kroese, F.G., Henning, R.H., 5'-AMP impacts lymphocyte recirculation
through activation of A2B receptors. J. Leukoc. Biol. 94 (2013) 89-98
Bronsema, K.J., Bischoff, R., Merbel, N.C. van de, High-sensitivity LC-MS/MS
quantification of peptides and proteins in complex biological samples: The impact of
enzymatic digestion and internal standard selection on method performance. Anal.
Chem. 85 (2013) 9528-9535
Budnik, L.T., Preisser, A.M., Permentier, H., Baur, X., Is specific IgE antibody analysis
feasible for the diagnosis of methylenediphenyl diisocyanate-induced occupational
asthma? Int. Arch. Occup. Environ. Health 86 (2013) 417-430
Christin, C., Hoefsloot, H.C.J., Smilde, A.K., Hoekman, B., Suits, F., Bischoff, R.,
Horvatovich, P., A critical assessment of feature selection methods for biomarker
discovery in clinical proteomics. Mol. & Cell. Proteom. 12 (2013) 263-276
Franciosi, L., Govorukhina, N., Fusetti, F., Poolman, B., Lodewijk, M.E., Timens, W.,
Postma, D., Hacken, N. ten, Bischoff, R., Proteomic analysis of human epithelial lining
Analytical Biochemistry › 17
fluid by microfluidics-based nanoLC-MS/MS: a feasibility study. Electrophoresis 34
(2013) 2683-2694
Happyana, N., Agnolet, S., Muntendam, R., Dam, A. van, Schneider, B., Kayser, O.,
Analysis of cannabinoids in laser-microdissected trichomes of medicinal Cannabis
sativa using LC-MS and cryogenic NMR. Phytochemistry 87 (2013) 51–59
Langenkamp, E., Kamps. J.A.A.M., Mrug, M., Verpoorte, E., Niyaz, Y., Horvatovich, P.,
Bischoff, R., Struijker-Boudier, H., Molema, G., Innovations in studying in vivo cell
behavior and pharmacology in complex tissues - microvascular endothelial cells in the
spotlight. Cell Tissue Res. 34 (2013) 647-669
Lo Tam Loi, A., Hoonhorst, S.J.M., Franciosi, L., Bischoff, R., Hoffmann, R.F., Heijink,
I., Oosterhout, A.J.M. van, Boezen, H.M., Timens, W., Postma, D.S., Lammers, J.W.,
Koenderman, L., Hacken, N.H.T. ten, Acute and chronic inflammatory responses
induced by smoking in individuals susceptible and non-susceptible to development of
COPD: from specific disease phenotyping towards novel therapy. Protocol of a crosssectional study. BMJ Open 3 (2013) e002178
Matusiak, N., Waarde, A.V., Bischoff, R., Oltenfreiter, R., Wiele, C.V., Dierckx, R.A.,
Elsinga, P.H., Probes for non-invasive matrix metalloproteinase-targeted imaging with
PET and SPECT. Curr. Pharm. Des. 19 (2013) 4647-4672
Merbel, N.C. van de, Vries, R. de, Aging of biological matrices and its effect on
bioanalytical method performance. Bioanalysis 5 (2013) 2393-2407
Meszaros, P., Klappe, K., Dam, A. van, Ivanovac, P.T., Milnec, S.B., Myers, D.S., Brown,
H.A., Permentier, H., Hoekstra, D., Kok, J.W., Long term myriocin treatment increases
MRP1 transport activity. Int. J. Biochem. Cell Biol. 45 (2013) 326-334
Ongay, S., Hermans, J., Bruins, A.P., Nieuwendijk, A.M.C.H., Overkleeft, H., Bischoff,
R., Electron transfer and collision induced dissociation of non-derivatized and
derivatized desmosine and isodesmosine. J. Am. Soc. Mass Spectrom. 24 (2013) 83-91
Roeser, J., Alting, N.F.A., Permentier, H.P., Bruins, A.P., Bischoff, R., Chemical
labeling of electrochemically cleaved peptides. Rapid Comm. Mass Spectrom. 27 (2013)
546-552
Roeser, J., Alting, N.F., Permentier, H.P., Bruins, A.P., Bischoff, R., Boron-doped
diamond electrodes for the electrochemical oxidation and cleavage of peptides. Anal.
Chem. 85 (2013) 6623-6632
Siegel, D., Permentier, H., Bischoff, R., 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. J. Chromatogr. A 1294 (2013) 87-97
Siissalo, S., Waard, H. de, Jager, M.H. de, Frijlink, H.W., Hinrichs, W., Dinter, H.,
Dam, A. van, Groothuis, G.M.M., Graaf, I.A.M. de, Nanoparticle formulation of a poorly
soluble CB-1 antagonist improves absorption by rat and human intestine. Drug Metab.
Dispos. 41 (2013) 1557-1565
Somborac-Bačura, A., Toorn, M. van der, Franciosi, L., Slebos, D.J., Žanić-Grubišić, T.,
Bischoff, R., Oosterhout, A.M.J. van, Cigarette smoke induces endoplasmic reticulum
stress response and proteasomal dysfunction in human alveolar epithelial cells. Exp.
Physiol. 98 (2013) 316-325
Analytical Biochemistry › 18
Suits, F., Fehniger, T.E., Vegvari, A., Marko-Varga, G., Horvatovich, P., Correlation
queries for mass spectrometry imaging. Anal. Chem. 85 (2013) 4398-4404
Wilffert, D., Reis, C.R., Hermans, J., Govoruhkina, N., Tomar, T., Jong, S. de, Quax,
W.J., Merbel, N.C. van de, Bischoff, R., Antibody-free LC-MS/MS quantification of
rhTRAIL in human and mouse serum. Anal. Chem. 85 (2013) 10754-10760
Ye, Y., Liu, H., Horvatovich, P., Chan, W., Liquid chromatography-electrospray
ionization tandem mass spectrometric analysis of 2-alkylcyclobutanones in irradiated
chicken by precolumn derivatization with hydroxylamine, J. Agricul. Food Chem., 61
(2013) 5758–5763
Recently published or accepted
Siegel, D., Permentier, H.P., Reijngoud, D.J., Bischoff, R. Chemical and technical
challenges in the analysis of central carbon metabolites by liquid-chromatography mass
spectrometry. J. Chrom. B (http://dx.doi.org/10.1016/j.jchromb.2013.11.022)
Ongay, S., Hendriks, G., Hermans, J., Berge, M. van den, Hacken, N. ten, Merbel, N.
van de, Bischoff, R., Quantification of free and total desmosine and isodesmosine in
human urine by LC-MS/MS: a comparison of the surrogate-analyte and the surrogatematrix approach for quantitation. J. Chrom. A
(http://dx.doi.org/10.1016/j.chroma.2013.12.035)
Horvatovich, P., Franke, L., Bischoff, R., Proteomic studies related to genetic
determinants of variability in protein concentrations. J. Proteome Res., 13 (2014), 5-14
Ourailidou, M.E., Meer, J.Y. van der, Baas, B.J., Jeronimus-Stratingh, M.,
Gottumukkala, A.L., Poelarends, G.J., Minnaard, A.J., Dekker, F.J., Aqueous oxidative
Heck reaction as a protein-labeling strategy. Chem.Bio.Chem.
(http://dx.doi.org/10.1002/cbic.201300714)
Fehniger, E. T., Suits, F., Végvári, A., Horvatovich, P., Foster, M., Marko-Varga, G.,
Queries of MALDI-MSI global datasets identifying ion mass signatures associated with
tissue compartments, Proteomics (accepted)
Hamon, E., Horvatovich, P., Marchioni, E., Aoudé-Werner, D., Ennahar, S.,
Investigation of potential markers of acid resistance in Lactobacillus plantarum by
comparative proteomics, accepted in J. Appl. Microbiol., 116 (2014), 134-144
Book & Special Topic Editors
Comprehensive biomarker discovery and validation for clinical application. P.L.
Horvatovich, R. Bischoff, Eds., RSC Publishing, Drug Discovery Series No. 33, 2013
Jong, G. de, Bischoff, R., Guest Editors special topic Analysis of Biopharmaceuticals in
Trends in Analytical Chemistry, vol. 48, July/August 2013, pp. 40-143
Analytical Biochemistry › 19
Book chapters
Horvatovich, P., Bischoff, R., Introduction to biomarker discovery and validation.
Preface In: Comprehensive biomarker discovery and validation for clinical application.
P. Horvatovich, R. Bischoff, Eds., RSC Publishing, Drug Discovery Series No. 33, 2013,
pp. V-VIII
Govorukhina, N., Bischoff, R., Sample preparation and profiling: Biomarker discovery
in body fluids by proteomics. In: Comprehensive biomarker discovery and validation
for clinical application. P. Horvatovich, R. Bischoff, Eds., RSC Publishing, Drug
Discovery Series No. 33, 2013, pp. 113-135
Horvatovich, P., Suits, F., Hoekman, B., Bischoff, R., Bioinformatics and statistics: LCMS(/MS) data preprocessing for biomarker discovery. In: Comprehensive biomarker
discovery and validation for clinical application. P. Horvatovich, R. Bischoff, Eds., RSC
Publishing, Drug Discovery Series No. 33, 2013, pp. 199-225
Merbel, N.C. van de, LC-MS bioanalysis of interconvertible compounds. In: Handbook
of LC-MS Bioanalysis: Best Practices, Experimental Protocols, and Regulations, First
Edition, W. Li, J. Zhang and F.L.S. Tse (Eds), John Wiley and Sons, 2013, pp 505-517
Non-peer reviewed
Horvatovich, P., Biomarkers, Independent Validation. In: Encyclopedia of Systems
Biology, Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki
Yokota, ISBN: 978-1-4419-9862-0 (Print) 978-1-4419-9863-7 (online), 2013, p. 126
Horvatovich, P., Biomarkers, Protein Expression. In: Encyclopedia of Systems Biology,
Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota, ISBN:
978-1-4419-9862-0 (Print) 978-1-4419-9863-7 (online), 2013, p. 127
Horvatovich, P., Biomarkers, Solid Tissue. In: Encyclopedia of Systems Biology,
Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota, ISBN:
978-1-4419-9862-0 (Print) 978-1-4419-9863-7 (online), 2013, p. 130
Jong, G. de , Bischoff, R., Editorial: Analysis of biopharmaceuticals. Trends in Anal.
Chem. 48 (2013) 40.
Lectures
Bischoff, R., Profiling and identification of cerebrospinal fluid proteins in a rat EAE
model of Multiple Sclerosis. University of Geneva, Switzerland, Jan. 25, 2013
Bischoff, R., From biomarker discovery to electrochemistry. University of Strasbourg,
France, March 11, 2013
Bischoff, R., From eQTLs to protein analyses in asthma and COPD. Proteomics Forum
2013, Berlin, Germany, March 17-21, 2013
Bischoff, R., Studying the MMP-9 – TIMP-1 protease-inhibitor system by activity-based
enrichment and selected reaction monitoring (SRM) nano-LC-MS/MS. 39th
International Symposium on High Performance Liquid Phase Separations and Related
Techniques (HPLC 2013), Amsterdam, The Netherlands, June 16-20, 2013
Analytical Biochemistry › 20
Bischoff, R., Electrochemistry – mass spectrometry in drug metabolism and protein
chemistry. EU-COST action CM1201, Zadar, Croatia, Sept. 10-13, 2013
Bischoff, R., Absolute quantitative LC-MS/MS analysis of rhTRAIL in serum. Advanced
Analytics for Therapeutic Proteins - from Research to Manufacturing, Dechema, Irsee,
Germany, Sept. 18-20, 2013
Bischoff, R., Wie het meet mag het zeggen!, Symposium on the occasion of the
retirement of Prof. Gerhardus (Ad) de Jong, Utrecht University, The Netherlands, Nov.
19, 2013
Boichenko A.P., Nano-chip-LC/MS for serum proteome profiling and cervical cancer
biomarker discovery, Dutch Society for Mass Spectrometry spring meeting, Bilthoven,
The Netherlands, April 11, 2013
Boichenko, A., Discovery and validation of serum biomarkers for cervical cancer by LCMS/MS. 39th International Symposium on High Performance Liquid Phase Separations
and Related Techniques (HPLC 2013), Amsterdam, The Netherlands, June 16-20, 2013
Boichenko A.P., Protein biomarkers for cervical cancer: from shotgun to targeted MS
quantification. 13th Netherlands Proteomics Platform Fall Meeting, Amsterdam, The
Netherlands, Nov. 8, 2013
Bronsema, K.J., High-sensitivity LC-MS/MS quantitation of peptides and proteins in
complex biological samples. Annual Meeting of the NWO/CW study group Analytical
Chemistry and COAST, the public-private partnership on Analytical Science &
Technology, Lunteren, The Netherlands, Nov. 20-21, 2013
Horvatovich, P., Current challenges in pre-processing of label-free LC-MS data of
complex proteomics samples. Université de Strasbourg, France, April 25, 2013
Horvatovich, P., Towards a comprehensive LC-MS proteomics data processing
platform. Skype presentation at 61st ASMS Conference on Mass Spectrometry and
Allied Topics, Minneapolis, USA, 9-13 June, 2013
Horvatovich, P., msCompare: A framework for quantitative processing and assessment
of LC-MS data. 1st International Conference on Profiling, Caparica, Portugal, Sept. 2-4,
2013
Horvatovich, P., C-HPP Wiki workshop. HUPO 2013 – 12th Annual World Congress,
Yokohama, Japan, Sept. 14-18, 2013
Horvatovich, P., Update on Chromosome 5. Kyoto HUPO Initiative Assembly, Kyoto,
Japan, Sept. 19, 2013
Merbel, N.C. van de, The value of an analytical result. MasterLab laboratory managers
meeting. Hoofddorp, The Netherlands, May 15, 2013
Merbel, N.C. van de, LC-MS as a platform for the quantitative bioanalysis of
biopharmaceutical proteins. FABIAN (the analytical challenge), Utrecht, The
Netherlands, Nov. 7, 2013
Merbel, N.C. van de, The usefulness of LC-MS as a platform for protein quantification,
from theory to practice. European Bioanalysis Forum, 6th Annual Open Symposium.
Barcelona, Spain, Nov. 20, 2013
Analytical Biochemistry › 21
Merbel, N.C. van de, Blood is no plasma: failing long-term frozen stability results for
cyclosporine A in diluted whole blood. European Bioanalysis Forum, 6th Annual Open
Symposium. Barcelona, Spain, Nov. 21, 2013
Ongay, S., Analysis of biomolecules on surfaces. TA-COAST, Lunteren, The
Netherlands, May 15, 2013
Wilffert, D., Quantitative UPLC – MS/MS of target proteins in serum. Spring meeting
KNCV Werkgroep Scheidingsmethoden, Sectie Analytische Chemie, Leiden, The
Netherlands, April 19, 2013
Poster presentations
Bischoff, R., Dutch Biomarker Development Center. LSH Plaza meeting, Utrecht, The
Netherlands, Jan. 31, 2013
Bischoff, R., Güzel, C., Govorukhina, N.I., Hoor, K. ten, Dekker, L.J.M., Hollema, H.,
Klip, H.G., Zee, A.G.J. van der, Luider, T.M., Cervix carcinoma proteomics: Biomarker
discovery in tissue by laser microdissection with biomarker validation in serum.
Proteomics Forum 2013, Berlin, Germany, March 17-21, 2013
Boichenko, A., Govorukhina, N., Zee, A. van der, Bischoff, R., 2D LC/MS separation of
tryptic peptides from human serum proteins using reversed-phase, strong cation
exchange, weak anion exchange and fused core fluorinated stationary phases. 39th
International Symposium on High Performance Liquid Phase Separations and Related
Techniques (HPLC 2013), Amsterdam, The Netherlands, June 16-20, 2013
Boichenko A.P., Govorukhina N., Zee A.G.J. van der, Bischoff R., Mass-spectrometry
based targeted quantification of cervical cancer related proteins in human serum,
Annual Meeting of the NWO/CW Studygroup Analytical Chemistry and COAST, the
public-private partnership on Analytical Science & Technology, Lunteren, The
Netherlands, Nov. 20-21, 2013
Bronsema, K., Bischoff, R., Merbel, N. van de, The role of internal standards in highsensitivity protein quantifications with LC-MS/MS. 39th International Symposium on
High Performance Liquid Phase Separations and Related Techniques (HPLC 2013),
Amsterdam, The Netherlands, June 16-20, 2013
Bronsema, K., Bischoff, R., Merbel, N. van de, The role of internal standards in highsensitivity protein quantifications with LC-MS/MS. European Bioanalysis Forum, 6th
Annual Open Symposium. Barcelona, Spain, Nov. 20-22, 2013
Govorukhina, N., Güzel , C., Bruin, A.I. de, Hoor, K.A. ten, Boichenko, A.P., Klip, H.G.,
Zee, A.G.J. van der, Luider, Th.M., Bischoff, R., Laser microdissection and cervix
carcinoma proteomics: translation of heat shock protein 90α as potential biomarker
candidate from tissue to serum. MSACL, San Diego, USA, Feb. 9-13, 2013
Gül, T., Permentier, H.P., Bischoff, R., Method development for electrochemical
synthesis of oxidative drug metabolites. ElCheMS (2nd International Workshop on
Electrochemistry/Mass Spectrometry), Münster, Germany, May 23-24, 2013
Gül, T., Permentier, H.P., Bischoff, R., Optimization of reaction parameters for
electrochemical oxidation of drug compounds with the Design of Experiments
technique. Annual Meeting of the NWO/CW study group Analytical Chemistry and
Analytical Biochemistry › 22
COAST, the public-private partnership on Analytical Science & Technology, Lunteren,
The Netherlands, Nov. 20-21, 2013
Güzel, C., Govorukhina, N., Hoor, K. ten, Dekker, L.J.M., Hollema, H., Klip, H.G., Zee,
A.G.J. van der, Boichenko, A., Luider, Th.M., Bischoff, R., Quantitation of low levels of
heat shock protein 90 in serum of cervical cancer patients by Selected Reaction
Monitoring. ASMS, Minneapolis, USA, June 9-13, 2013
Güzel, C., Govorukhina, N., Hoor, K. ten, Dekker, L.J.M., Hollema, H., Klip, H.G., Zee,
A.G.J. van der, Boichenko, A., Luider, Th.M., Bischoff, R., Cervix carcinoma
proteomics: Biomarker discovery in tissue by laser microdissection, Proteomics Forum
2013, Berlin, Germany, March 17-21, 2013
Hoekman, B., Christin, C., Hoefsloot, H., Smilde, A., Breitling, R., Suits, F., Bischoff, R.,
Horvatovich, P., Critical assessment of LC-MS data pre-processing and feature
selection methods for biomarker discovery in clinical proteomics. Proteomics Forum
2013, Berlin, Germany, March 17-21, 2013
Horvatovich, P.L., Chromosome-centric human protein project chromosome 5. HUPO
2013 – 12th Annual World Congress, Yokohama, Japan, Sept. 14-18, 2013
Mitra, V., Govorukhina, N., Zwanenburg, G., Smilde, A., Reijmers, T., Westra, I., Suits,
F., Bischoff, R., Horvatovich, P., Experimental design for complex proteomics samples
using ASCA. NPC 10th anniversary conference: 10 Years Progress in Proteome Biology,
Utrecht, The Netherlands, Feb. 11-12, 2013
Ongay, S., Langelaar, M., Groothuis, G., Bischoff, R., Development of a new tissue
fixative: towards facilitating proteomic analysis on fixated tissue. Annual Meeting of
the NWO/CW study group Analytical Chemistry and COAST, the public-private
partnership on Analytical Science & Technology, Lunteren, The Netherlands, Nov. 2021, 2013
Prely, L., Oldenburger, A., Hermans, J., Paal, K., Castelli, R., Merbel, N.C. van de,
Oosterhout, A.J.M. van, Overkleeft, H.S., Schmidt, M., Bischoff, R., Studying the MMP9 – TIMP-1 protease-inhibitor system by activity-based enrichment and selected
reaction monitoring (SRM) nano-LC-MS/MS. 39th International Symposium on High
Performance Liquid Phase Separations and Related Techniques (HPLC 2013),
Amsterdam, The Netherlands, June 16-20, 2013
Pruim, P., Hilhorst, M., Hendriks, G., Hillewaert, V., Vries, R. de, Verhaeghe, T.,
Merbel, N. van de, An improved LC-MS/MS method for the determination of
artemether and dihydroartemisinin in human plasma. European Bioanalysis Forum, 6th
Annual Open Symposium. Barcelona, Spain, Nov. 20-22, 2013
Rozeveld, D., Bischoff, R., Oosterhout, A. van, Heijink, I., ADAM10 plays a crucial role
in house dust mite-induced release of chemokine ligand CCL20 by airway epithelium.
American Thoracic Society International Conference 2013, Philadelphia, USA, May 1722, 2013
Wilffert, D., Rodrigues dos Reis, C.R., Hermans, J., Govorukhina, N., Tushar, T., Jong,
S. de, Quax, W.J., Merbel, N.C. van de, Bischoff, R., Quantitative, antibody-free LCMS/MS analysis of recombinant tumor necrosis factor-related apoptosis-inducing
ligand (TRAIL) in serum. 39th International Symposium on High Performance Liquid
Phase Separations and Related Techniques (HPLC 2013), Amsterdam, The
Netherlands, June 16-20, 2013
Analytical Biochemistry › 23
Wilffert, D., Rodrigues dos Reis, C.R., Hermans, J., Govorukhina, N., Tushar, T., Jong,
S. de, Quax, W.J., Merbel, N.C. van de, Bischoff, R., Quantitative, antibody-free LCMS/MS analysis of recombinant tumor necrosis factor-related apoptosis-inducing
ligand (TRAIL) in serum. Annual Meeting of the NWO/CW study group Analytical
Chemistry and COAST, the public-private partnership on Analytical Science &
Technology, Lunteren, The Netherlands, Nov. 20-21, 2013
Yang, Y., Ongay, S., Kema, I., Bischoff, R., Specific enrichment of 3-nitrotyrosine–
containing peptides for biomarker discovery. 39th International Symposium on High
Performance Liquid Phase Separations and Related Techniques (HPLC 2013),
Amsterdam, The Netherlands, June 16-20, 2013
Yuan, T., Permentier, H.P., Bruins, A.P., Bischoff, R., Modified electrodes applied in the
investigation of drug metabolism. ElCheMS (2nd International Workshop on
Electrochemistry/Mass Spectrometry), Münster, Germany, May 23-24, 2013
Zhang, T., Permentier, H.P., Bischoff, R., Specific enrichment method for
electrochemically cleaved peptides. ElCheMS (2nd International Workshop on
Electrochemistry/Mass Spectrometry), Münster, Germany, May 23-24, 2013
Zhang, T., Permentier, H.P., Bischoff, R., Development of a specific enrichment method
for electrochemically cleaved peptides. Annual Meeting of the NWO/CW study group
Analytical Chemistry and COAST, the public-private partnership on Analytical Science
& Technology, Lunteren, The Netherlands, Nov. 20-21, 2013
Miscellaneous:
Bischoff, R., Coordinator of the Division Medicinal Chemistry and Bioanalysis of the
Groningen University Institute of Drug Exploration (GUIDE)
Bischoff, R., Board of Examiners, TopMaster in Medical and Pharmaceutical Drug
Innovation for the Graduate School of Medical Sciences (University of Groningen)
Bischoff, R., Director: Mass Spectrometry Center of the Faculty of Mathematics and
Natural Sciences (University of Groningen)
Editorial Tasks
Bischoff, R., Executive Editor, J. Chromatogr. B (Elsevier)
Horvatovich, P.L., Editorial Board Member, J. Proteome Res. (ACS)
Horvatovich, P.L. and Bischoff, R., invited editors of the book “Proteomics biomarker
discovery and validation for clinical applications" published by the Royal Society of
Chemistry of the United Kingdom
Merbel, N.C. van de, Editorial Board Member, Bioanalysis (Future Science)
Scientific Advisory Functions:
Bischoff, R., Board Member, Dutch Proteomics Platform
Analytical Biochemistry › 24
Bischoff, R., Board Member, Working Group Pharmaceutical and Biomedical Analysis
of the Royal Dutch Chemical Society (KNCV)
Horvatovich, P., Secretary of the Dutch PhD student (AIO) Network Analytical
Chemistry
Merbel, N.C van de, Harmonization team leader of the Global Bioanalysis Consortium
(GBC)
Seminars
Prof. Dr. Herbert Oberacher, Innsbruck Medical University, Innsbruck, Austria:
Forensic applications of high resolution mass spectrometry. March 8, 2013
Prof. Dr. Manfred Wuhrer, VU University Amsterdam, Amsterdam, The Netherlands:
Clinical glycomics of autoimmune diseases and cancer. May 7, 2013
Prof. Dr. Bernd Bodenmiller, University of Zurich, Switzerland: Mass cytometry to
study single cell signaling in biology and disease. June 11, 2013
Awards
Third price best poster competition at the European Bioanalysis Forum, 6th Annual
Open Symposium, Barcelona, Spain, 20-22 November 2013: Bronsema, Bischoff,
Merbel van de, The role of internal standards in high-sensitivity protein quantifications
with LC-MS/MS.
Agilent Best Poster Award (by the board of expert reviewers), 39th International
Symposium on High Performance Liquid Phase Separations and Related Techniques
(HPLC 2013), Amsterdam, The Netherlands, June 16-20, 2013: Wilffert, Reis,
Hermans, Govorukhina, Tomar, de Jong, Quax, van de Merbel, Bischoff, Quantitative,
Antibody-Free LC-MS/MS Analysis of Recombinant Tumor Necrosis Factor-Related
Apoptosis-Inducing Ligand (TRAIL) in Serum.
Analytical Biochemistry › 25
Research:
Funded Projects:
Netherlands Proteomics Center II - Bioinformatics in proteomics (Topic E4)
Project title: Quantitation, processing and classification algorithms for mass
spectrometry (E 4.2)
Principal Investigator:
Prof. Dr. Peter Horvatovich
Funding Period: 2009-2013
Netherlands Proteomics Center II – New separation and enrichment tools in
proteomics (Topic: E1)
Project title: Affinity Enrichment of Proteins and Peptides (E 1.3)
Principal Investigator:
Prof. Dr. Rainer Bischoff
Funding Period: 2009-2013
NWO Centres for Systems Biology Research (CSBR)
Systems Biology Centre for Energy Metabolism and Ageing
Principal Investigator:
Prof. Dr. Bert Groen (University Medical Center Groningen)
Funding Period: 2010-2015
NWO-STW 11056
Innovative analytical methodologies for biopharmaceuticals
Principal Investigator:
Prof. Dr. Rainer Bischoff (University of Groningen)
Funding Period: 2011-2015
Dutch Cancer Society (KWF) RUG-2011-5021
Biomarkers for cervical cancer: from discovery to the clinic
Principal Investigator:
Prof. Dr. Rainer Bischoff (University of Groningen)
Funding Period: 2011-2015
NWO-ACTS/TA-COAST 053.21.104
Analysis of biomolecules on surfaces (BIOSURF)
Principal Investigator:
Prof. Dr. Rainer Bischoff (University of Groningen)
Funding Period: 2012-2015
NWO-STW 11957
Electrochemistry – Mass Spectrometry (EC-MS) for proteomics and drug metabolism
Principal Investigator:
Prof. Dr. Rainer Bischoff (University of Groningen)
Funding Period: 2012-2016
NWO-ECHO 711.012.006
Electrochemically-assisted redox enzyme reactors by cofactor immobilization
Principal Investigator:
Prof. Dr. Marco Fraaije (University of Groningen)
Funding Period: 2012-2016
Analytical Biochemistry › 26
EU-COST Action CM1201
Biomimetic radical chemistry
Principal Investigator:
Prof. Dr. Chrys Chatgilialoglu (University of Bologna, Italy)
Dutch representatives on the management team:
Prof. Dr. Frank Dekker
Prof. Dr. Rainer Bischoff
Funding Period: 2012-2016
Chromosome-Centric Human Proteome Project (C-HPP)
Principal Investigators:
Prof. Dr. Young-Ki Paik (Yonsei University, Seoul)
Prof. Dr. György Marko-Varga (Lund University, Sweden)
Prof. Dr. William S. Hancock (Northeastern University, Boston, USA)
Responsible scientists for Chromosome 5 (the “Dutch Chromosome”)
Prof. Dr. Rainer Bischoff
Prof. Dr. Peter Horvatovich
Period: 2012-2022
SNN project T3041
Ontwikkeling van LC-MS/MS als platformtechnologie voor de bioanalyse van eiwitten
Principal investigator:
Prof. Dr. Nico C. van de Merbel
Funding Period: 2013-2017
NWO-STW Perspectief program P12-04
Biomarker Development Center (Biomarker-DC)
Principal investigator:
Prof. Dr. Rainer Bischoff
Co-investigators:
Dr. Theo M. Luider & Dr. Arfan Ikram (Erasmus Medical Center, Rotterdam)
Prof. Dr. Alain van Gool & Prof. Dr. Ron Wevers (Radboud University Medical Center,
Nijmegen)
Dr. Nick ten Hacken (University Medical Center Groningen)
Funding Period: 2014-2019
Analytical Biochemistry › 27
Teaching
Bachelor projects
Biostatistics (bachelors)
FATEM
Biotechnology (masters)
Industrial Bioanalysis (masters)
MFO (Medisch-Farmaceutisch Onderzoek)
Proteomics/Genomics (bachelors)
Medical Genomics & Proteomics (bachelors)
Introduction to proteomics (Faculty of
Pharmacy, University of Strasbourg)
TI-COAST course on Biomarkers (national
master’s program)
Behavioural and Cognitive Neurosciences
(international masters)
Medical and Pharmaceutical Drug Innovation
(TopMasters)
Mass Spectrometry (open course)
Pharmaceutical Analysis C (bachelors)
Drug Development (masters)
Nov. 19, 2012 – Feb. 1, 2013
Apr. 24 – June 28, 2013
Nov. 11 – Feb. 2014
March 25 – 22 April 2013
June 11 – July 15, 2013
Feb. 24, 2013
March 5, 2013
March 4 – March 22, 2013
March 27, 2013
April 17 – May 4, 2013
May 21 – June 10, 2013
April 24, 2013
April 27, 2013
Nov. 12, 2013
Nov. 22, 2013
Nov. 4 – 5, 2013
Sept. 2 – Oct. 11, 2013
Sept. 9, 2013
P.L. Horvatovich, member of the ‘opleidingscommissie’
J.W. Meints, member of the ‘ontwikkelteam Farmacie’
Analytical Biochemistry › 28
Outlook
Many colleagues and friends have contributed to another exciting year of research,
teaching and last not least to shouldering many other tasks. This time I would like to
thank especially Hjalmar Permentier and Jos Hermans, who were indispensable in
organizing the move to the new facilities at the ERIBA research institute.
2014 will see the start of the Biomarker Development Center as well as the
continuation of Biopharmaceuticals research line with renewed funding. The extended
capabilities at the new facilities should allow us to establish new collaborations and to
attract funding. I am particularly excited about the Medicinal Chemistry and
Bioanalysis (MCB) program that promises already now to be a stimulus for research
collaborations. Peter Horvatovich has taken the lead in the Chromosome-Centric
Human Proteome Project and first concrete research activities are on the horizon albeit
that funding is still pending.
I want to take this opportunity to thank all co-workers for their excellent work in
2013 as well as the many collaborators in and outside the University of Groningen for
pleasant and efficient collaborations.

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