analytical biochemistry, annual report 2012

faculty of mathematics and natural sciences

department of pharmacy

Analytical Biochemistry

Annual Report 2012 Prof.Dr. Rainer Bischoff 25 February 2013

Analytical Biochemistry › 2

Group photo Analytical Biochemistry Back row: Daniël Wilffert, Peter Horvatovich, Turan Gül, David Siegel, Hjalmar Permentier, Alexander Boychenko, Tao (Larry) Zhang Middle Row: Sara Ongay Camacho, Kees Bronsema, Jos Hermans, Natalia Govorukhina, Nico van de Merbel, Vikram Mitra, Karin Wolters, Yun Yang Front row: Jan Willem Meints, Jolanda Meindertsma, Tao Yuan, Rainer Bischoff 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


Members of the Research Group: Staff: Prof. Dr. Rainer Bischoff Dr. Peter Horvatovich Dr. Natalia Govorukhina Jos Hermans Jan Willem Meints Jolanda Meindertsma (secretary; 0.4 fte) Prof. Dr. Nico van de Merbel (professor through special appointment) Post-doctoral researchers: Dr. Alexander Boychenko Dr. Sara Ongay Camacho Dr. Krisztina Paal (until Jan. 31, 2012) Dr. Karin Wolters Dr. David Siegel (start May 01, 2012) Ph.D. students: Kees Bronsema Lorenza Franciosi Berend Hoekman (group Horvatovich) Vikram Mitra (group Horvatovich) Laurette Prely Julien Roeser (defence on March 08, 2013) Daniël Wilffert Yun Yang Turan Gül (start Sep. 01, 2012) Tao Yuan (start Oct. 01, 2012) Tao (Larry) Zhang (start Oct. 01, 2012) Research Students: Anneloes De Bruin, start Sep. 1, 2011, end April 24, 2012 Jakub Radzikowski, start March 2, 2012, end August 08, 2012 Jennifer Schlaman, start Sept. 1, 2012


Overview 2012

The year 2012 saw a considerable increase of our activities in the area of combining Electrochemistry with Mass Spectrometry. Two new PhD students started funded by a grant from the Dutch Technology Foundation (STW) and another PhD student joined this project line with a Scholarship from the Chinese Government (CSC). We furthermore started a collaboration with the group of Prof. Marco Fraaije at the Biology Department based on a joint excellence in chemical research (ECHO) grant from the Dutch Research Organization (NWO) in the area of immobilized enzymes on electrode surfaces.

Our contribution to the Systems Biology project on Energy Metabolism and Ageing increased in 2012 with the start of David Siegel as postdoctoral researcher focusing on metabolite analysis. Karin Wolters, a postdoctoral researcher focusing on the proteomics aspects of this project, has made great strides in developing some 350 targeted, quantitative protein assays based on LC-MS/MS in the Selected Reaction Monitoring (SRM). Together with colleagues from the Biology Department and the University Medical Center we expect to harvest concrete results from this work in 2013.

Some of the “old” projects have also seen progress, for example our search for biomarkers for the early diagnosis of Cervical Cancer. Thanks to funds from the Dutch Cancer Society and the Netherlands Genomics Initiative and our collaboration with Prof. Ate van der Zee (University Medical Center) and Dr. Theo Luider (Erasmus Medical Center, Rotterdam) we are now in a phase of validating a number of candidates that we discovered by tissue (laser-guided microdissection) and serum analysis. This progress would not have been possible without the dedicated work of Natalia Govorukhina and Alexander Boichenko.

The year 2012 has seen considerable progress in our more recent research line focusing on the analysis of Biopharmaceutical Proteins. Daniël Wilffert, who started his PhD on the analysis of Tumor necrosis factor- Related Apoptosis – Inducing Ligand (TRAIL) in serum has developed a method that reaches the low ng/mL level without the help of antibodies. Kees Bronsema (Pharmaceutical Research Associates (PRA) in Assen) advanced in his work on the effect of internal standards on the analysis of proteins in plasma and serum and is well on his way to finalize a number of sensitive LC-MS/MS assays in the SRM mode for recombinant “Nanobodies” (collaboration with Ablynx) and clinically relevant biomarkers (collaboration with Prof. Ido Kema, UMCG).

These are a few highlights to give you an impression of what has been and is going on in the group. Next to initiating new projects and having young researchers starting, we also assembled a consortium of excellent researchers to try and update our mass spectrometry facility through an NWO-Groot (meaning BIG) grant application. Despite very positive referee comments and a successful site visit, we finally did not get this prestigious grant, which came as a disappointment to everyone involved. Despite this setback we are looking forward to moving to our new lab on the top floor of the ERIBA (European Research Institute on the Biology of Ageing) building, where we will establish an integrated Analytical Biochemistry – Mass Spectrometry laboratory by bringing highly qualified personnel together. If all goes well, I expect that a couple of PhD theses will be finalized in 2013 (Julien Roeser has his date set for March 08 already) and that all projects will deliver a constant flow of high-quality publications as they did in 2012. It is noteworthy that the group of Peter Horvatovich delivered two top publications in Molecular and Cellular Proteomics related to data processing and statistical data analysis, areas that are all too often neglected in the field of proteomics. I wish you interesting reading of this Annual Report and a successful year 2013. In case you see possibilities for future collaborations, I would be happy to discuss them with you.

Resear

1. Cervic The cer(UMCG) athat are acBoychenkoDutch Can Project D Cervicawhile in thwomen. Indetect bioserum and Currenttargeted tiend colleaHSP-90 indevelopedQ-TOF mencouragin

Nehave initiaof tissue fanalysis. Tand separa

rch Proje

cal Cance

rvical cancerand Theo Luctively involo in Groninncer Society

Descriptio

al carcinomhe developinn this projemarkers fo

d tissue analt work focuissue analygues in Rot

n serum at t a quantitat

mass spectrng (see belo

xt to validaated anothefrom cance

To enhance ation metho

ects

er Biomar

r project is uider (Erasmlved in this gen and Co

y (KWF).

on

ma is the seng countrieect, we are

or the earlylyses.

uses on valiysis after lastterdam devhe ng/mL ltive method

rometer. Wow).

ating biomaer round of er patients proteome ods at the p

rkers

run in collamus Univer project are

oskun Guzel

econd most es cervical ce developingy diagnosis

idating biomser-guided veloped a taevel withoud for serum

While valida

arker candi discovery w and controcoverage weptide and

aboration wsity Medica Natalia Govl in Rotterda

frequent ccarcinoma isg new apprand progn

marker canmicrodisse

argeted nanut the use of

m markers bation is st

ROC curvstage III-Ibased onbiomarkeserum. Ar

idates in a work basedols as well

we are develat the prote

with the groual Center, Rovorukhina aam. The pro

carcinoma is the most froaches basosis of cerv

ndidates thaection or senoLC-MS/Mf antibodies

based on natill ongoing

ve for discrimV patients fr LC-MS/MS r-candidate-rea under the

larger set o on laser-gul as on a mloping betteein level.

Analytical B

ups of Ate votterdam). and Alexandoject is fund

in women wfrequent cased on LC-vical cancer

at were diserum analysMS method ts. The GronianoLC-MS/Mg, initial r

minating cervrom healthy c(SRM modederived pepte ROC curve

of serum sauided micromore in-deer sample p

Biochemistry › 5

an der Zee Coworkers der ded by the

worldwide, rcinoma in

-MS/MS to r based on

covered by sis. To this to measure ingen team MS using a results are

vical cancer controls ) of a tide in e is 0.86.

amples, we odissection

epth serum preparation


2. Data processing and statistical analysis (group Horvatovich) This research line is carried out by two PhD students Vikram Mitra and Berend Hoekman under the supervision of Peter Horvatovich. We expect that Vikram Mitra and Berend Hoekman will defend their theses in 2013. The fruitful collaboration with Frank Suits from IBM continued and resulted in a submitted publication on a data pre-processing pipeline for MALDI imaging analysis. Other manuscripts are currently undergoing final revision. Collaboration with the Laboratoire de Chimie Analytique et Sciences de l’Aliment (Strasbourg, France) resulted in one publication with two other submitted manuscripts on the topic of biomarker discovery to identify Lactic bacilli with probiotic properties. Peter Horvatovich is editing a book on “Comprehensive Biomarker Discovery and Validation for Clinical Application” to be published by the Royal Chemistry Society (UK) with Rainer Bischoff as co-editor. Peter Horvatovich is actively involved as member of the Chromosome 5 team of the Chromosome Centric Human Proteome Project and in an STW grant application to develop a bioinformatics platform for the detection of low abundant peptides and proteins. Project Description The analysis of complex mixtures with hyphenated analytical methods like LC-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 was published in Molecular & Cellular Proteomics. This manuscript was prepared in close collaboration with our 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 LC-MS and finalized the development of a liquid chromatography gradient optimization method to improve identification efficiency within a given chromatography analysis of complex proteomics samples. Though Ishtiaq Ahmad, is working at UvA, 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 groups.

Vikram Mitra finalized his project to develop a generic time alignment algorithm which is able to determine if two LC-MS chromatograms can be aligned with respect to peak elution order inversion and a sufficient number of common peaks (paper submitted). Vikram is at the final stage of evaluating an approach to analyse data sets obtained from an experimental design study to reveal the importance of pre-analytical factors affecting the profile of complex shotgun proteomics samples. This 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 in complex LC-MS(/MS) data sets. In the meantime, Vikram obtained a job at Proteome Sciences plc (London, UK) starting on April 01.


3. Activity-dependent analysis of metalloproteases The work on this project is currently on hold, since funding ran out in 2012. I am currently seeking renewed funding to continue this exciting project line. Project Description The project has the goal of developing activity-based profiling methods for metalloproteases with a special focus on matrix metalloproteases (MMPs) and the membrane-bound members of this enzyme family. Among membrane-bound metalloproteases, we focus our attention on the ADAMs family of enzymes. ADAMs (A Disintegrin And Metalloproteinase) are membrane-bound zinc dependent proteins. Several members of the ADAM family are catalytically active and capable of releasing biologically active proteins from their membrane-anchored proform by proteolytic cleavage (so-called shedding). Deregulation of this catalytic activity is potentially linked to various disease states such as rheumatoid arthritis, M. Alzheimer, cancer metastasis and remodeling of tissue such as in heart failure or asthma. The work of Laurette Prely (PhD student) in 2012 was finalized with developing a method for quantifying MMP9 (active and pro-forms) and the major endogenous inhibitor TIMP-1 in in cell culture supernatant after exposure to cigarette smoke by LC-MS/MS (SRM) (manuscript in preparation). Assessing the activation/inhibition status of MMP-9 is now possible based on quantification of all major components of this protease – anti-protease system. We believe this to be a promising approach to assess the activation of enzyme systems that rely on pro-enzyme conversion for their activation.


4. Electrochemistry – Mass Spectrometry This project is a collaboration between the Analytical Biochemistry group, the Mass Spectrometry Center (Hjalmar Permentier), the Biotechnology group (Marco Fraaije) and the University of Twente (Albert van den Berg and Wouter Olthuis). Four new PhD students started in Groningen focusing on the electrochemical cleavage of peptides and proteins (Larry Zhang), the semi-preparative electrochemical synthesis of Phase-I drug metabolites (Turan Gül), the surface modification of electrodes (Tao Yuan) and the immobilization of FAD-dependent monooxygenases (Marzena Krzek, group Fraaije). The previous work on electrochemical peptide bond cleavage by Julien Roeser has led to a thesis that will be defended on March 08, 2013. The project is being funded by the Dutch Technology Foundation (STW), the Dutch Research Organization (NWO, ECHO grant, collaboration Fraaije) and the Chinese Scholarship Council (CSC). 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. All PhD students started recently and work on this project has resumed slowly. Output from earlier work has, however, resulted in a number of publications notably in the field of drug metabolism and peptide cleavage and capture.

Reaction of electrochemically generated spirolactones LW+14 (A) and LY-2 (B) with hexylamine under basic conditions (from Roeser et al., Rapid Comm. Mass Spectr., 27 (4), 546-552 (2013)).

5. ProfilsusceptiDisease This prour group with DirkjInstitute o Project D Proteomsampled in(patient oridentified performedisotope labacute effecawait furth

iTRAQ repoyoung non-individuals young susc

ing of epiible or no (COPD)

roject was f early 2012je Postma,

of the Unive

Descriptio

mics of ELn the lung dr volunteer) 300-400 pd a pilot stubelling follocts of smokher validatio

orter ion patt-susceptible at baseline (

ceptible indiv

ithelial lion-suscep

funded by t. It is a mu Nick ten H

ersity Medic

on

F is a novduring bron) from well-

proteins in Eudy with 4 owed by a me on ELF. Ton.

tern of a biomindividuals a(Peak 2), youviduals at bas

ning fluidptible to C

the TopInstulti-center pHacken andcal Center G

el approachnchoscopy s-defined locELF from a COPD patimore extensThis resulte

marker that cafter acute smung susceptiseline (Peak

d (ELF) fChronic O

titute Pharmproject primd Antoon v

Groningen (U

h. ELF hasso that 3 prcations. Folla COPD patients and 4sive study id in a numb

changes in abmoking (Peakble individua4).

from smoObstructiv

ma (TIP) anmarily perfovan OosterhUMCG).

s the advanrobes can belowing our itient and a 4 healthy vointo COPD ber of biom

bundance bek 1), young n

als after acute

Analytical B

okers thatve Pulmo

nd the workrmed in col

hout from t

ntage of bee obtained pinitial workhealthy vol

olunteers u susceptibili

marker cand

etween a gronon-susceptie smoking (P

iochemistry › 9

t are onary

k ended in llaboration the GRIAC

eing locally per subject

k, where we lunteer, we sing stable ity and the

didates that

oup of ible Peak 3) and

6. Proteo This prour group with groupestablished Project D Approvdepressionweight gaiinto the bipsychoactiinhibitor agoal to ininduced co A sampbeen estabHoekman proteins, aWe are cur

Effect of anrelated to d

omics in

roject was f early 2012p of Anton Sd an animal

Descriptio

ved drug mn (e.g. assoin or weightiochemical ive side effeand since investigate ch

onditions veple preparablished. Dat resulting a number ofrrently final

n anti-epilepsdrug-induced

relation t

funded by t. It is a muScheurink (l model of d

on

molecules agociated witht loss. They mechanismects. Since ansulin-signahanges of tersus controation methota processinin 17.000

f which sholizing this w

sy and an anobesity.

to drug-in

the TopInstulti-center p(Departmendrug-induce

gainst convh schizophry are therefoms of obesityat least one aling may bthe proteomols in differodology forng of this c identified

ow clear up-work with ta

ti-depressive

nduced w

titute Pharmproject primnt of Biologed weight al

vulsions (erenia) have ore of great y and to de group of m

be involved me and theent organs.r proteomiccomplex da peptides - or down-rargeted vali

e drugs on pr

weight alt

ma (TIP) anmarily perfogy, Universitlterations.

.g. associat as side eff interest to

evelop anti-molecules se

in the obsee phosphop cs based on

ata set was leading to

regulation ddation expe

rotein expres

Analytical Bio

terations

nd the workrmed in colty of Gronin

ted with epfects that th obtain furt-obesity drueems to act erved effect

proteome un

n 2D-LC-Mperformed ca. 1000

due to drug eriments.

ssion in the l

ochemistry › 10

k ended in llaboration ngen), who

pilepsy) or hey induce ther insight ugs without as a kinase ts, it is our nder drug-

MS/MS has by Berend identified treatment.

iver of rats

7. Studydifferent This wowe study ionization chemical p Project D The mecompoundelectrosprareversed-paltogetherbe marked Jos andusing bothfar investalthough s Sara hdifferent rJASMS inmechanismmolecular

(A) Chemicstructures oNHS (MeO-(MeO-dPEGMass Spec

ying the Et derivati

ork is perfothe effect response o

properties.

Descriptio

etabolome ods that aray ionizatio

phase chror. Earlier wodly enhanced Sara contih mass spectigated physome correlaas further

reagents andn 2013). Tms and is weight com

cal structuresof the derivat-EPr-NHS), mG(8)-NHS) e

ctrom., 24, 83

Electrosprization re

ormed by Joof differen

of low-mole

on

of any organre not amon (ESI). Fuomatographork showeded by coupliinued invesctrometric aysico-chemiations have endeavourd studied th

This work one of the

mpounds.

s of desmosintization reagemediumPEGmployed for

3-91 (2013)).

ray Ionizaeactions

os Hermannt chemicalecular weig

nism contamenable tourthermore,hic stationd that especing polyethystigating theand physicoical param

e been foundred to derihe CID and

sheds more first exam

ne (DES, leftents, from to

G-OPFP (penDES/IDS de

.

ation Res

ns and Sara derivatizin

ght metabol

ains many loo high-sen, these comary phase

cially the ioyleneglycol e mechanismo-chemical

meters fully d. ivatize desm ETD fragmre light on

mples wher

t) and isodesop to bottom:ntafluorophenerivatization (

sponse in

Ongay Camng reagentslites in rela

ow-moleculsitivity LCpounds ares and thunization eff derivativesms underlymeasureme explains

mosine anmentation be

n the respre ETD has

smosine (IDS propionic annyl-activated(from Ongay

Analytical Bi

n relation

macho. In ts on the el

ation to the

lar weight hC-MS analye often not rus escape ficiency upos to these coying this enhents. None the observ

d isodesmoehaviour (pupective frags been use

S, right). (B) nhydride, sho PEG), longP

y et al., J. Am

ochemistry › 11

to

this project lectrospray ir physico-

hydrophilic ysis using retained on detection on ESI can ompounds. hancement of the thus ved effects

osine with ublished in gmentation ed for low-

Chemical ortPEG-PEG-NHS

mer. Soc.

8. Protei As part(SBC-EMAmethodoloMS/MS infellow, whmain metanow focus under diffsystems bHjalmar P Project D Standara so-calledsubsequentechniquesapproach molecules recently thset of so-caRelated tothe yeast SConcurren

Targeted prmonitoring quantificatio

TheWe are cupreparing

in and m

t of the SystA) Karin Wogy that is bn the selecteho started inabolites inv on applyinferent cond

biology modPermentier.

Descriptio

rd proteomd ‘shotgun’

nt fragments in a datain the qua in complexhere has beealled “prote

o systems bSaccharom

ntly we are a

roteomics in workflow, (Bon of the targ

e metaboliturrently ab a global sta

metabolite

tems BiologWolters (pobased on foled reaction n May 201

volved in enng these metditions of endelling. Bot

on

mics is prima’ approach tation by c-dependentantitative ax samples, en consider

eotypic” or “iology we h

myces cerevialso develop

the selectedB) definition ogeted peptide

te analyticable to quanable isotope

e analysis

gy Center foostdoctoralllowing a wi monitoring2, developenergy metathods to agnergy usagth postdocs

arily based requiring collision-indt way. LC-Manalysis of for examplrable progre“signature” have now qisiae and wping SRM a

d reaction moof time windoes.

al work is alntify some e-labeled int

for syste

or Energy M researcheide range ofg (SRM) moed LC-MS/Mbolism. Wieing yeast ce and phys

s work in t

on profilingthe selecti

duced dissoMS/MS in tlow levels le, for drugess in quan peptides in

quantitative will apply thassays for th

onitoring (SRows in sched

lso based o70 metabo

ternal stand

ems biolo

Metabolismer) establishf protein-spode. David MS methodith both appcells and mosical activitthe MS Cor

g as many pion of precociation or the SRM m of low-mog analysis i

ntifying protn biological assays for

hem to an ahe mouse m

RM) mode. (Auled SRM an

n LC-MS/Molites and adard in yeas

Analytical Bio

gy

and Ageinghed protei

pecific pepti Siegel, a podology to quproaches inouse modelty to providre Facility

peptides as cursor ions other frag

mode is a wolecular wein blood serteins based samples usi some 35o pageing mododels.

A) The selectnd (C) relativ

MS in the Sare in the st.

ochemistry › 12

g Research in analysis ides by LC-ostdoctoral uantify the n place, we ls of ageing de data for headed by

possible in and their

gmentation widely used

ight target rum. More on a given ing SRM. proteins in el of yeast.

ted reaction ve

SRM mode. process of

f

9. LC(biophar In collaAmsterdamwork on dGroningenligand (TR This prNico van dhigh sensiin close co Project D Proteintherapeutidevelop thof analyticto follow th In a coNetherlanhighly senDaniël WilWim Quaxfirst methoreaches ngvivo pharm

Center Grsensitivitysystematicattributes

C-MS/MSrmaceuti

aboration wm (Wilfrieddifferent asn is to studyRAIL) in colroject is clode Merbel), tivity analy

ollaboration

Descriptio

n pharmaceic agents th

hese macromcal methodshem in vivo

onsortium bds, instrum

nsitive and lffert (PhD x) study varod for serumg/mL sensimacokinetic

roningen (Jy of 10 pg/mc evaluation (see J. Chro

S anacals) in c

with Utrechd Niessen, G

pects of thy variants olaboration w

osely linked who is dev

ysis of biophn with the bi

on

euticals orhat are rapidmolecules ins that can co during clinbetween lea

ment manuselective m student) anriants of TRm analysis iitivity withoc study in m

Jos KosterimL for a pen of the effeom. B, 893-

alysis complex b

ht UniversitGovert Somshe analysis of the tumowith the gro

d with the Pveloping quaharmaceuticioanalytical

r “biopharmdly increasinto effectivecharacterizenical develoading acadefacturers a

methods for nd Carlos R

RAIL in bodis currentlyout the use

mice.

ink, UMCGeptide pharect of inter-894, 1-14, (

of prbiological

ty (Ad de Jsen) and a nof protein r necrosis foup of WimPhD projectantitative Lcals with a f laboratory

maceuticalsing in releve and safe pe them at thopment andemic group

and pharma biopharma

Reis (postdody fluids andy in its finale of antibod

Calibrabetwee20 ng/m The pultra-speptidbiomamode analyscalled extendmonocwith Depart

G). Recentlyrmaceuticalrnal standar(2012))

rotein l matrices

Jong) and tnumber of ibiopharma

factor-relatem Quax.

t of Kees BLC-MS/MS m

focus on pe of PRA (As

s” form a vance for heproducts it ihe moleculad in clinical pps in analytaceutical coaceutical anoctoral resead cell culturl stage of vadies and wi

ation curve ofen 20 ng/mLmL).

project of Ksensitive, qude phar

rkers by LCand mor

is of single nanobodied this workclonal antib

the Htment of thy Kees reacl. His workrds on anal

Analytical Bio

pharmas

the Free Unindustrial pceuticals. Ted apoptosi

ronsema (smethods foeptides and ssen).

class of ealth care. Iis necessaryar level andpractice. tical chemiompanies wnalysis. In Garcher in thre by LC-M

alidation. Thll be applie

f TRAIL in seand 20 µg/m

Kees focusuantitative rmaceuticalC-MS/MS inre recently-chain antibes). It is pk to the a

bodies in colHospital he Universiched a con

k focuses fulytical meth

ochemistry › 13

ceuticals

niversity of partners we The task in is-inducing

supervision r the ultra- antibodies

innovative In order to

y to dispose d that allow

stry in the we develop Groningen, he group of

MS/MS. The his method ed to an in

erum mL (LLOQ =

ses on the analysis of ls and n the SRM y on the bodies (so-planned to analysis of llaboration Pharmacy

ity Medical ncentration urther on a hod quality

f

f

f

f


10. Development of reversible crosslinkers for histochemistry and proteomics

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 also 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 embedded tissue due to the 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).

Our initial aim is to develop reversible chemical crosslinkers that can be cleaved under specified conditions followed by extending this principle to crosslinkers with added functionalities, for example for easier protein quantification or enrichment. As the project is in its initial phase, we will report first results in the next annual report.


Ph.D. projects: J. Roeser LC/on-chip-electrochemistry/mass spectrometry in (bio)analytical chemistry, drug metabolism and proteomics (focus on proteomics) Promotor: Prof. Dr. R. Bischoff Co-promotors: Dr. A.P. Bruins, Dr. H.P. Permentier (Mass Spectrometry Core Facility) Start: November 2006 Defense date: March 08, 2013 B. Hoekman Development of a comprehensive data processing and statistical analysis methodology for label-free LC-MS data in biomarker discovery Promotor: Prof. Dr. R. Bischoff Co-promotors: Dr. P.L. Horvatovich, 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), Prof. Dr. N.H.T. ten Hacken (UMCG) Supervisor: Dr. N. Govorukhina Start: February 2008 L. Prely A chemical proteomics approach towards profiling and imaging of metalloprotease activity Promotors: Prof. Dr. R. Bischoff, Prof. Dr. A.J.M. van Oosterhout (UMCG) Supervisor: Dr. K.A. Paal Start: February 2008 V. Mitra Quantitation, processing and classification algorithms for mass spectrometry Promotors: Prof. Dr. R. Bischoff, Prof. Dr. A.K. Smilde (University of Amsterdam) Co-promotor: Dr. P.L. Horvatovich 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 Drug Metabolism and Protein Chemistry Promotors: Prof. Dr. R. Bischoff, Prof. Dr. I. Kema (UMCG) Supervisor: Dr. H. Permentier Start: September 2012 Turan Gül Electrochemistry – Mass Spectrometry (EC-MS) for Proteomics and Drug Metabolism Promotor: Prof. Dr. R. Bischoff Supervisor: Dr. H. Permentier Start: September 2012 T. Yuan Electrochemistry combined with mass spectrometry to study drug metabolism Promotor: Prof. Dr. R. Bischoff Supervisor: Dr. H. Permentier Start: October 2012


Scientific Output 2012 Scientific publications: Peer-reviewed Avanti, C., Permentier, H.P., Dam, A. van, Poole, P., Jiskoot, W., Hinrichs, W.L.J., Frijlink, H.W., Stabilization of the disulfide bond of oxytocin in citrate buffered solution by divalent metal ions. Molecular Pharmaceutics 9 (2012) 554-562 Bischoff, R., Schlüter, H., Amino-acids: Chemistry, functionality and selected non-enzymatic post-translational modifications. J. Proteomics 75 (2012) 2275-2296 Bronsema, K.J., Bischoff, R., Merbel, N.C. van de, Internal standards in the quantitative determination of protein biopharmaceuticals using liquid chromatography coupled to mass spectrometry. J. Chromatogr. B 893-894 (2012) 1-14 Gandhi, T., Puri, P., Fusetti, F., Breitling, R., Poolman, B., Permentier, H.P., The effect of iTRAQ labeling on relative abundance of peptide fragment ions produced by MALDI. J. Proteome Res. 11 (2012) 4044–4051 Geurink, P.P., Prely, L.M., Marel, G.A. van der, Bischoff, R., Overkleeft, H.S., Photoaffinity labeling in activity-based protein profiling. Topics in Current Chemistry 324 (2012) 85-113 Hamon, E., Horvatovich, P., Bisch, M., Bringel, F., Marchioni, E., Aoudé-Werner, D., Ennahar, S., Investigation of biomarkers of bile tolerance in lactobacillus casei using comparative proteomics. J. Proteome Res. 11 (2012) 109-118 Hoekman, B., Breitling, R., Suits, F., Bischoff, R., Horvatovich, P., msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative biomarker studies. Mol. Cell. Proteom., 11 (6) (2012); doi:10.1074/mcp.M111.015974 Krzeslak, J., Papaioannou, E., Merkerk, R. van, Paal, K.A., Bischoff, R., Cool, R.H., Quax, W.J., Lipase A gene transcription in Pseudomonas alcaligenes is under control of RNA polymerase δ54 and response regulator LipR. FEMS Microbiol. Lett. 329 (2012) 146-153 Merbel, N.C. van de, Bronsema, K.J., Nemansky, M, Protein quantification by LC-MS: can it make a difference? Bioanalysis 4 (2012) 2113-2116 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. Internatl. J. Biochem. & Cell Biology 45 (2012) 326-334 Nouri-Nigjeh, E., Vries, M.P. de, Bruins, A.P., Bischoff, R., Permentier, H.P., Electrochemical oxidation of quaternary ammonium electrolytes: Unexpected side reactions in organic electrochemistry. Electrochem. Commun. 21 (2012) 54-57 Nouri-Nigjeh, E., Bruins, A.P., Bischoff, R., Permentier, H.P., Electroanalytic oxidation of hydrogen peroxide on a platinum electrode in the imitation of oxidative drug metabolism of lidocaine. Analyst 137 (2012) 4698-4702 Ongay, S., Boichenko, A., Govorukhina, N., Bischoff, R., Glycopeptide enrichment and separation for protein glycosylation analysis. J. Sep. Sci 35 (2012) 2341-2372


Prely, L.M., Paal, K., Hermans, J., Heide, S. van der, Oosterhout, A.J.M. van, Bischoff, R., Quantification of matrix metalloprotease-9 in bronchalveolar lavage fluid by selected reaction monitoring with microfluidics nano-liquid-chromatography-mass spectrometry. J. Chromatogr. A 1246 (2012) 103-110 Rosenling, T., Stoop, M.P., Attali, A., Aken, H. van, Suidgeest, E., Christin, C., Stingl, C., Suits, F., Horvatovich, P., Hintzen, R.Q., Tuinstra, T., Bischoff, R., Luider, T.M., Profiling and identifcation of cerebrospinal fluid proteins in a rat EAE model of multiple sclerosis. J. Proteome Res. 11 (2012) 2048-2060 Siegel, D., Applications of reversible covalent chemistry in analytical sample preparation. Analyst 137 (2012) 5457-5482 Stoop, M. P., Rosenling, T., Attali, A., Meesters, R. J. W., Stingl, C., Dekker, L. J., van Aken, H., Suidgeest, E., Hintzen, R. Q., Tuinstra, T., van Gool, A., Luider, T. M., and Bischoff, R., Minocycline Effects on the Cerebrospinal Fluid Proteome of Experimental Autoimmune Encephalomyelitis Rats. J. Proteome Res. 11 (2012) 4315-4325 Recently published or accepted Boichenko, A., Govorukhina, N., van der Zee, A. G., and Bischoff, R. (2013) Simultaneous serum desalting and total protein determination by macroporous reversed-phase chromatography. Anal. Bioanal. Chem., DOI 10.1007/s00216-013-6749-9 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? Internatl. Arch. Occupational and Environmental Health, (2012), DOI:10.1007/s00420-012-0772-6 Christin, C., Hoefsloot, H. C. J., Smilde, A. K., Hoekman, B., Suits, F., Bischoff, R., and Horvatovich, P. (2013) A Critical Assessment of Feature Selection Methods for Biomarker Discovery in Clinical Proteomics. Mol. Cell. Proteom. 12, 263-276 Lo Tam Loi, A. T., Hoonhorst, S. J. M., Franciosi, L., Bischoff, R., Hoffmann, R. F., Heijink, I., van Oosterhout, A. J. M., Boezen, H. M., Timens, W., Postma, D., Lammers, J. W., Koenderman, L., and ten Hacken, N. H. T. (2013) 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 cross-sectional study. BMJ Open 3, 10.1136/bmjopen-2012-002178 Matusiak, N., van, W. A., Bischoff, R., Oltenfreiter, R., Van De Wiele, C., Dierckx, R. A., and Elsinga, P. H. (2013) Probes for non-invasive matrix metalloproteinase-targeted imaging with PET and SPECT. Curr. Pharm. Des., accepted (PMID: 23339739) Ongay, S., Hermans, J., Bruins, A. P., Nieuwendijk, A. M., Overkleeft, H., and Bischoff, R. (2013) Electron transfer and collision induced dissociation of non-derivatized and derivatized desmosine and isodesmosine. J. Am. Soc. Mass Spectrom. 24, 83-91 Roeser, J., Alting, N. F. A., Permentier, H. P., Bruins, A. P., and Bischoff, R. P. H. (2013) Chemical labeling of electrochemically cleaved peptides. Rapid Communications in Mass Spectrometry 27, 546-552


Somborac-Bacura, A., van der Toorn, M., Franciosi, L., Slebos, D. J., Zaniç-Grubisiç, T., Bischoff, R., and van Oosterhout, A. J. (2013) Cigarette smoke induces ER stress response and proteasomal dysfunction in human alveolar epithelial cells. Experim. Physiol. 98, 316-325 Book chapters Dekker, F., Abello, N., Wisastra, R., and Bischoff, R. (2012) Enrichment and Detection of Tyrosine-Nitrated Proteins, In: Current Protocols in Protein Science, John Wiley & Sons, Inc., Chapter 14, Unit 14.13 Non-peer reviewed Horvatovich, P., Bischoff, R., Discovery and validation of protein biomarkers. Europ. Pharm. Review, Issue / 10 July 2012 Wolters, K. Permentier, H., Bischoff, R., Targeted proteomics as a tool to study aging in yeast. NPC Highlights, 15, May 2012, pp 16-19 European Proteomics Association Issue 6, Dec. 2012: Chromosome Centric Human Proteome Project - The Chromosome 5 Consortium Lectures: Bischoff, R., Analysis of biomolecules on surfaces (BioSurf). NWO TransACTS Symposium, Lunteren, The Netherlands, January 31 – February 01, 2012 Bischoff, R., Studying the MMP-9 proteolytic system by tandem mass spectrometry in the SRM Mode. NVMS/BSMS International Congress on Mass Spectrometry, Rolduc, The Netherlands, March 29-31, 2012 Bischoff, R., Comparative analysis of serum and tissue samples from cervical cancer patients for biomarker discovery. 12th Annual Symposium Proteo, Sherbrooke, Canada, May 18, 2012 (invited lecture) Bischoff, R., Analysis of complex biological samples: a challenge for separation science, mass spectrometry and bioinformatics. European Lab Automation 2012, Hamburg, Germany, May 30 – 31, 2012 (invited lecture) Bischoff, R., Quantitative proteomics in biomarker discovery and validation. HPLC 2012; 38th International Symposium on High Performance Liquid Phase Separations and Related Techniques, Anaheim, CA, USA, June 16-21, 2012 (invited lecture) Bischoff, R., Quantitative LC-MS/MS analysis of biopharmaceuticals. DSM Biologics, Groningen, The Netherlands, June 26, 2012 Bischoff, R., Amino Acids: Chemistry, functionality and selected post-translational protein modifications. European Proteomics Association (EuPA 2012) Scientific Congress: new horizons and applications for proteomics, Glasgow, United Kingdom, July 09-12, 2012 (invited tutorial)


Bischoff, R., Acute and chronic inflammatory responses induced by smoking in individuals being susceptible and non-susceptible to the development of COPD: from specific disease phenotyping towards novel tailor-made therapy. GRIAC Retraite, Garnwerd, The Netherlands, September 14, 2012 Bischoff, R., Minocycline effects on the CSF proteome of experimental autoimmune encephalomyelitis rats. FIGON Dutch Medicine Days, Lunteren, The Netherlands, October 2, 2012 Bischoff, R., Profiling and identification of cerebrospinal fluid proteins in a rat EAE model of multiple sclerosis. 7th MS-Pharma Day, Rome, Italy, October 22-24, 2012 (invited lecture) Bischoff, R., Activity-based proteomics of metalloproteases. Proteomics Beyond IDs, 4th Annual Meeting of Proteomics Society, India, CSIR-National Chemical Laboratory, Pune, India, November 22-24, 2012 (invited keynote lecture) Boychenko, O., Serum profiling of cervical cancer patients for biomarker discovery using stable-isotope labeling and label-free quantitation. Pharmacy Day (University of Groningen), Groningen, The Netherlands, May 10, 2012 Bronsema, K.J., Comparing the performance of different internal standards in the LC-MS/MS quantification of peptides and proteins. Waters Technology Days, Utrecht, The Netherlands, October 12, 2012 Bronsema, K.J., Work-flows and internal standards in high sensitivity peptide and protein quantifications with LC-MS/MS. Symposium “Het zelfde spoor”, Utrecht, The Netherlands, November 15, 2012 Govorukhina, N., Biomarker discovery for cervical cancer. NPC progress meeting, Utrecht, The Netherlands, February 7, 2012 Horvatovich, P., Current challenges in pre-processing of label-free LC-MS data of complex proteomics samples. Hong Kong University of Science & Technology, Hong Kong, February 17, 2012 Horvatovich, P., Current challenges in pre-processing of label-free LC-MS data of complex proteomics samples. Dalian Institute of Chemical Physics, Dalian, China, February 22, 2012 Horvatovich, P., Current challenges of label-free quantitative proteomics. NBIC Hot Topic series in “Peptide and protein quantification using mass spectrometry”, Utrecht, the Netherlands, March 5, 2012 Horvatovich, P., Bioinformatics aspect of label-free LC-MS comprehensive profiling technology. Select Biosciences - Indian Lab Automation 2012, October 30-31, 2012 Merbel, N.C. van de, Stability assessment in regulated bioanalysis. Global Bioanalysis Consortium meeting, San Antonio, TX, USA, March 30, 2012 (invited lecture) Merbel N.C. van de, It’s only just begun: the importance of sample preparation for protein quantification by LC-MS, European Bioanalysis Forum 5th open Symposium, Barcelona, Spain, November 14, 2012.


Ongay, S., Polyethylenglycol-labeling as a strategy to increase electrospray ionization efficiency for metabolomic applications. Pharmacy Day (University of Groningen), Groningen, The Netherlands, May 10, 2012 Ongay Camacho, S., Electron transfer and collision induced dissociation of non-derivatized and derivatized desmosine and isodesmosine: a mechanistic study. Annual Meeting of the NWO/CW Studygroup Analytical Chemistry and COAST, the public-private partnership on Analytical Science & Technology, November 21-22, Lunteren, The Netherlands Wilffert, D., Absolute quantitative LC-MS/MS analysis of TRAIL. Pharmacy Day, Groningen, The Netherlands, May 10, 2012 Wolters, J.C., Targeted proteomics to study replicative aging in yeast. Pharmacy Day (University of Groningen), Groningen, The Netherlands, May 10, 2012 Wolters, J.C., Targeted proteomics in energy metabolism and ageing. Netherlands Proteomics Platform fall meeting, Amsterdam, The Netherlands, November 30, 2012 Yang, Y., Specific enrichment of 3-nitrotyrosine–containing peptides. Pharmacy Day (University of Groningen), Groningen, The Netherlands, May 10, 2012 Poster presentations: Ahmad, I., Hoekman, B., Lukasse, P., Suits F., Breukelen B., Kampen A.H.C. van, Olabarriaga S.D., Bruin, F. de, Bischoff R., America, T., Moerland P.D., Horvatovich P., Galaxy workflow for analysis of label-free LC-MSn data for comparative biomarker studies. NPC progress meeting, Utrecht, The Netherlands, February 7, 2012 Boichenko, A.P., Govorukhina,N., Bruin, A. de, Zee, A.G.J. van der, Bischoff, R., Cancer biomarker discovery in serum. EMBO Practical Course in "Mass Spectrometry and Proteomics" (European Molecular Biology Organization), Odense, Denmark, April 18-25, 2012 Boichenko, A.P., Govorukhina, N., Zee, A.G.J. van der, Bischoff, R., Label and label-free serum proteomic profiling for cervical cancer biomarker discovery and validation. Annual Meeting of the NWO/CW Studygroup Analytical Chemistry and COAST, the public-private partnership on Analytical Science & Technology, Lunteren, The Netherlands, November 21-22, 2012 Govorukhina, N.I., Boichenko, A.P., Bruin, A. de, Zee, A.G.J. van der Zee, Bischoff, R., Comparative analysis of serum samples from cervical cancer patients for biomarker discovery using iTRAQ labeling. NPC progress meeting, Utrecht, The Netherlands, February 7, 2012 Mitra, V., Suits, F., Smilde, A. K., Hoefsloot, H. C. J., Bischoff, R., Horvatovich, P., CheckAlign for complex LC-MS proteomics data. NPC progress meeting 2012, Utrecht, The Netherlands, February 7, 2012 Mitra,V., Hoefsloot, H., Smilde, A., Suits, F., Bischoff, R., Horvatovich, P., Peak elution order inversion: main obstacle for time alignment of complex proteomics LC-MS datasets. HUPO 11th Annual World Congress, Boston, A, USA, September 9-13, 2012 Mitra,V., Hoefsloot, H., Smilde, A., Suits, F., Bischoff, R., Horvatovich, P., Peak elution order inversion: main obstacle for time alignment of complex proteomics LC-MS


datasets. Annual Meeting of the NWO/CW Studygroup Analytical Chemistry, Lunteren, The Netherlands, November 21-22, 2012 Ongay, S., Hermans, J., Nieuwend, R., Overkleeft, H., Bischoff, R. Etd vs cid fragmentation of non-labeled and labeled desmosine and isodesmosine. NVMS-BSMS International congress on mass spectrometry, Rolduc, The Netherlands, March 28-30, 2012 Rosenling, T., Stoop, M.P., Horvatovich, P.L., Luider, T.M., Bischoff, R., Proteomic analysis of cerebrospinal fluid in a rat model of multiple sclerosis. Sample handling and biomarker discovery & validation. 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20 - 24, 2012 Siegel, D., Permentier, H., Bischoff, R., Comprehensive quantification of energy metabolites by UPLC-MS/MS. Annual Meeting of the NWO/CW Studygroup Analytical Chemistry and COAST, the public-private partnership on Analytical Science & Technology, Lunteren, The Netherlands, November 21-22, 2012 Suits, F., Vegvari, A., Fehniger, T., Marko-Varga, Gy., Horvatovich, P., An Interactive Environment for Guided Discovery of Biomarkers in Imaging Mass Spectrometry. 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20 - 24, 2012 Wolters, J.C., Permentier, H.P., Bischoff, R., Targeted proteomics to study aging in yeast. 60th ASMS Conference on Mass Spectrometry and Allied Topics, Vancouver, Canada, May 20 - 24, 2012 Wolters, J.C., Meinema, A.C., Janssens, G.E., Ciapaite, J., Heinemann, M., Veenhoff, L.M., Bakker, B.M., Permentier, H.P., Bischoff, R., Targeted proteomics to study aging. SBC-EMA meeting, Groningen, The Netherlands, September 24, 2012 Yang, Y., Ongay, S., Kema, I., Bischoff, R., Specific enrichment of 3-nitrotyrosine–containing peptides. Annual Meeting of the NWO/CW Studygroup Analytical Chemistry and COAST, the public-private partnership on Analytical Science & Technology, Lunteren, The Netherlands, November 21-22, 2012 Miscellaneous: Bischoff, R., Coordinator for the Division Synthesis and Analysis for the Graduate School of Medical Sciences (University of Groningen) 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 Core Facility of the Faculty of Mathematics and Natural Sciences Bischoff, R., Expert reviewer for different funding agencies and a number of scientific journals Horvatovich, P.L. and Bischoff, R., invited editors for the book “Proteomics biomarker discovery and validation for clinical applications" by the Royal Society of Chemistry of the United Kingdom Horvatovich, P.L., Expert reviewer for various funding agencies and a number of scientific journals


Merbel, N.C van de, Harmonization team leader of the Global Bioanalysis Consortium (GBC) Editorial Boards: Bischoff, R., Executive Editor, J. Chromatogr. B (Elsevier) Merbel, N.C. van de, Editorial Board Member, Bioanalysis (Future Science) Scientific Advisory Functions: Bischoff, R., Board Member, Dutch Proteomics Platform Bischoff, R., Co-Theme Leader (Netherlands Proteomics Center II): New Separation and Enrichment Tools in Proteomics Bischoff, R., Board Member, Working Group Pharmaceutical and Biomedical Analysis of the Royal Dutch Chemical Society (KNCV) Horvatovich, P., Theme Leader (Netherlands Proteomics Center II): Bioinformatics in Proteomics Horvatovich, P., Secretary of the Dutch PhD student (AIO) Network Analytical Chemistry Seminars: Dr. Diego Millo, Free University Amsterdam, Biomedical Analysis and Spectroscopy: Spectroelectrochemical analysis of intact microbial biofilms for sustainable energy production. April 23, 2012


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: 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 TopInstitute Pharma T1-108 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 (COPD) Principal Investigator: Prof. Dr. Dirkje Postma (University Medical Center Groningen, UMCG) Funding Period: 2008-2012 TopInstitute Pharma T2-105 Investigation of drug induced weight alterations to identify novel therapeutic strategies for the treatment of obesity, dyslipidemia and diabetes Principal Investigator: Dr. Elwin Verheij (TNO) Funding Period: 2008-2012 NWO-STW 08008 A chemical proteomics approach towards profiling and imaging of metalloprotease activity Principal Investigator: Prof. Dr. Rainer Bischoff (University of Groningen) Funding Period: 2008-2012 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 EU-COST Action CM1201 Biomimetic radical chemistry Principal Investigator: 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 Dr. Peter Horvatovich Prof. Dr. Manfred Wuhrer (Free University of Amsterdam) Prof. Dr. Henry Lam (University of Hongkong) Period: 2012-2022


Teaching Bachelor projects Nov. 21, 2011 – Feb. 3, 2012

Feb. 13, 2012 – Apr. 17, 2012 Apr. 25, 2012 – June 29, 2012 Nov. 19, 2012 – Feb. 1 2013

Biostatistics (bachelors) March 26, 2012 – Apr. 17, 2012 June 12, 2012 – July 2, 2012

Biotechnology (masters) Feb. 28, 2012 Behavioural and Cognitive Neurosciences (masters)

Nov. 27, 2012

Medical and Pharmaceutical Drug Innovation (TopMasters class)

Nov. 20, 2012

Mass Spectrometry (open course) Dec. 18-19, 2012 Pharmaceutical Analysis C (bachelors) Sept. 7 – Nov. 9, 2012 Drug Development (masters) Sept. 10, 2012 Introduction to proteomics (Faculty of Pharmacy, University of Strasbourg)

Apr. 20, 2012

P.L. Horvatovich, member of the ‘opleidingscommissie’ J.W. Meints, member of the ‘ontwikkelteam Farmacie’


Outlook Many colleagues and friends have contributed to another exciting year of research, teaching and last not least to shouldering many administrative tasks. This time I would like to thank especially Jan Willem Meints, who is indispensable for running our bachelor courses in Pharmaceutical Analysis C and Biostatistics next to supervising some of the Bachelor Projects.

2013 will be an exciting year as we will be moving to new facilities in the European Research Institute on the Biology of Ageing (ERIBA) to form an integrated Analytical Biochemistry – Mass Spectrometry group with closer links to the Clinical Chemistry group at the UMCG. We also hope to make a good start with the Chromosome-Centric Human Proteome Project and notably the many possibilities that this world-wide network offers.

I want to take this opportunity to thank all co-workers for their excellent work in 2012 as well as the many collaborators in and outside of Groningen for the pleasant and efficient collaborations.

analytical biochemistry, annual report 2012

Documents