Former student research projects

Eva van Hees, Msc Leiden University, Life Science & Technology,
March 2019 – August 2019
Determining the effect of splenectomy on total serum IgG Fc-glycosylation by LC-MS
Supervised by Iwona Wojcik, David Falck

Coen de Jong, MSc VU Amsterdam
February 2019 – June 2019
EPO glycopeptide analysis with MALDI-FTICR-MS
Supervised by Steffen Lippold, Noortje de Haan

Sanne Pot, Analytical Chemistry MSc+, UVA-VU, Amsterdam
November 2018 – July 2019
Supervised by Elena Dominguez Vega

Mariachristina Festa, MSc University of Pisa, Pisa Italy
October 2018 – July 2019
N-glycan MSI of pT1-CRC
Supervised by Fanny Boyaval, Bram Heijs

Nadi el Hajjouti, BSc Hogeschool InHolland Amsterdam
September 2018 – January 2019
Performance test MALDI-TOF-MS and MALDI-FTICR-MS
Supervised by Noortje de Haan, Bram Heijs, Hans Dalebout

Leandra Mulder, MSc Radbout University, Nijmegen
August 2018 – March 2018
MSI-based proteomic and lipidomic investigation of myxoid liposarcoma
Supervised by Bram Heijs, prof. dr. Judith Bovée (PATH)

Wouter Zijderveld, MSc Leiden University, Leiden
April 2018 – October 2018
Improving sample preparation for on- tissue digestion MALDI-MSI of proteolytic peptides
Supervised by Bram Heijs

Marit Hoogendoorn, BSc Leiden University Medical Centre, Leiden
April 2018 – September 2018
Mass spectrometry imaging of lipids in multiple sclerosis
Supervised by Bram Heijs

Sarila Rambaks, University of Applied Science (HLO) Rotterdam
February 2018 – June 2018
Het opzuiveren van post-ranslationeel gemodificeerde eiwitten
Supervised bij Paul Hensbergen

Esmee Schoof, Master Biomedical Sciences, LUMC
Proteomic analysis of aberrant glycosylation in human cancer cell lines
January 2018 – July 2018
Supervised by Martina Pirro, Paul Hensbergen

Tineke Blom, BSc Leiden University of Applied Sciences, Leiden
October 2017 – February 2018
Site-specific glycosylation analysis of haptoglobin from human serum using LC-MS
Supervised by Viktoria Dotz, Jelena Simunovic

Martha Ingola, MSc University of Oulu, Oulu Finland
September 2017 – April 2018
MALDI-MSI based investigation of radiation sensitivity in chondrosarcoma
Supervised by Bram Heijs, prof. dr. Judith Bovée

Inge Dekker, University of Applied Science (HLO) Leiden
June 2017 – December 2017
Evaluation and optimization of a small scale proteomic sample preparation procedure for LC-MS/MS based proteomics
Supervised by Paul Hensbergen, Peter van Veelen

Jennifer Heikamp, BSc Leiden University of Applied Sciences
May 2017 – February 2018
Method development for N-glycan profiling of immunoglobulin G and total plasma proteins
Supervised by Viktoria Dotz, Gerda Vreeker, Albert Bondt

Floris-Jan de Graaff, BSc Hogeschool Leiden, Leiden
May 2017 – February 2018
Mass spectrometry imaging of lipids in multiple sclerosis
Supervised by Bram Heijs

Maria Elena Castellani, MSc VU Amsterdam.
March 2017 – November 2017
Linkage specific sialic acid stabilization and internal standardization of plasma N-glycans for high-throughput negative-mode MALDI-TOF-MS analyses
Supervised by Noortje de Haan and Karli Reiding

Audunn Rúnar Gissurarson, School of Health Sciences, University of Iceland
February 2017 – April 2017
Sample preparation strategies for breast cancer studies: Focus on a 1-acid glycoprotein by means of MALDI-ToF mass spectrometry
Supervised by Marco Bladergroen, Yuri van der Burgt, Wilma Mesker (Surgery department)

Corné van der Plas,
February 2017 – July 2017
Method development for released glycan purification based on HILIC SPE
Supervised by: Gerda Vreeker

Tamás Pongrász, Medical Biotechnology University of Pécs, MSc.
January 2017 –
Exploring the coupling of CE to FT-ICR and its usefulness for intact protein analysis
Supervised by: Guinevere Kammeijer and Simone Nicolardi

Jayshri Murli, MSc
November 2016 –
Purification of IgG/IgA from salvia and analysis of tryptic glycopeptides using LC-MS
Supervised by: Rosina Plomp, Viktoria Dotz

Shane Soogea, MSc VU Amsterdam.
September 2016 – August 2017
The effects of a high-fat diet on the lgG N-glycosylation in FcRy and C3 protein knockout mice
Supervised by Noortje de Haan, Viktoria Dotz

Pablo Mohaupt, MSc VU Amsterdam
September 2016 – March 2017
Linkage-specifc sialic acid derivatization combined with reducing end labeling enables CE separation and sensitive ESI-MS detection of released N-glycans
Supervised by: Noortje de Haan

Sander Wagt, Analytical Chemistry, VU University, Amsterdam, MSc.
August 2016 – April 2017
Exploring the possibilities for isomer separation of glycans and glycopeptides using “zero-flow” separation with CE-ESI-MS
Supervised by: Guinevere Kammeijer

Tatiana Shamorkina, University of Applied Science (HLO), Leiden
August 2016 – May 2017
Characterization of the activity and specificity of a novel Pro-Pro endopeptidase (PPEP-2) from Paenibacillus alvei.
Supervised by Paul Hensbergen

Alexandre Mau, MSc
May 2016 – September 2016
Analysis of short chain fatty acids in the synovial fluid of arthritis patients
Supervised by: Martin Giera

Shivani Kapoerchan, Leiden University, MSc
April 2016 – November 2016
Glycosylation of saliva- and serum-derived IgG and IgA
Supervised by: Rosina Plomp, Noortje de Haan, Viktoria Dotz

Valentina Cordò, Leiden University, MSc
February 2016-August 2016
Mass spectrometry-based analysis of protein phosphorylation in the human pathogen Clostridium difficile
Supervised by: Paul Hensbergen

Mike Filius, MSc VU Amsterdam,
Feb 2016 – Sept 2016
Towards a PVDF membrane based derivatization protocol
Supervised by: Noortje de Haan

Sarah Azaabal, Analytical Chemistry, VU Amsterdam, MSc
November 2015 – July 2016
Native glycoprotein analysis mainly by using CESI-MS(/MS)
Supervised by: Guinevere Kammeijer and Isabelle Kohler

A. J. Khalil, Leiden University, BSc
April 2015 – August 2015
Investigations on the influence of culture conditions on the N-glycan profile of colorectal cancer cell lines
Supervised by: Stephi Holst

Mahmoud Habeeb, Leiden University, Pre-master
April 2015 – August 2015
Immunoglobulin G purification with human specific Fc beads and N-Glycan analysis using MALDI-TOF-MS
Supervised by: Albert Bondt

Lisette den Hertog, Leiden University, Bsc
March 2015 – July 2015
IgG and IgA N-glycosylation profiling in human serum
Supervised by: Rosina Plomp

Stefan Rademaker, Hogeschool Utrecht, Bsc
Februari 2015 – October 2015
‘Biases in the Peptide-N4-(N-acetyl-β-glucosaminyl) Asparagine Amidase F digestion of Immunoglobulin’ & ‘Application of glycopeptide amidation to Erythropoeitin glycopeptides’
Supervised by: David Falck

Wouter de Wilde, VU Amsterdam, MSc
Februari 2015 – August 2015
Supervised by: Martin Giera

Marieke Heijink, VU Amsterdam, MSc
Januari 2015 – August 2015
Supervised by: Martin Giera

Thomas Idzinga, Delft U/Leiden U, BSc
Februari 2015-June 2015
A GC-MS method for the analysis of short chain fatty acids in fecal samples
Supervised by: Martin Giera

Gerda Vreeker, VU Amsterdam, Msc
December 2014 – July 2015
Reducing end derivatization for N-glycan analysis by MALDI-TOF-MS
Supervised by: Karli Reiding

Thomas Volder, Hogeschool Inholland Amsterdam, Bsc
September 2014 – Februari 2015
Biases in the Peptide-N4-(N-acetyl-β-glucosaminyl) Asparagine Amidase F digestion of Immunoglobulin G
Supervised by: David Falck

Fatima Boulahkrif, VU University, MSc
April 2014 – October 2014
Short chain fatty acid analysis using GC-MS
Supervised by: Martin Giera

A.J.M. Deuss, VU Amsterdam, Msc
Februari 2014 – August 2014
Towards a comprehensive glycomics comparison of colorectal cancer cell lines – Glycomic signatures of malignancy and metastasis
Supervised by: Stephi Holst

Adriana Sanna, Leiden, MSc BW
Februari 2014 – July 2014
Quantification of c-di-GMP in Clostridium difficile; linking a second messenger with proteins involved in adhesion and motility.
Supervised by: Paul Hensbergen

Mica Menks, VU Amsterdam, MSc BW
Februari 2014 – July 2014
Characterization of Clostridium difficile sortase activity and specificity.
Supervised by: Paul Hensbergen

Coen de Jong, Hogeschool Leiden, Bsc
Jan 2014 – Jul 2014
Development of glycomics methods and their clinical application,
Supervised by: Albert Bondt

Noortje de Haan, VU Amsterdam, Msc
November 2013 – Aug 2014
Comprehensive glycopeptide profiling using carboxilic acid derivatization for the linkage-specific stabilization of sialic acids
Supervised by: Karli Reiding

Vakil Takhaveev & Matvey Zakharov, Moscow State UNiversity, MSc Bioinformatics
July 2013 – August 2013,
Investigating the role of mass measurement error tolerance in peptide identification
Supervised by: Magnus Palmblad and Alex Henneman

Hester Stekelenburg, VU Amsterdam, MSc Bioinformatics
September 2013 – May 2014
Using unidentified MS1 peptide signals to improve protein abundance quantification accuracy
Supervised by: Alex Henneman

Marije Kuipers-Wensveen, Leiden University, BSc
July 2013 – November 2013
Adrenic Acid as lipoxygenase substrate and its influence on stimulated human neutrophils
Supervised by: Martin Giera

Dennis Kuijper, VU Amsterdam, Msc
April 2013 – October 2013
Linkage-specific stabilization of sialic acids using DMT-MM/methanol for glycan analysis by MALDI-TOF-MS
Supervised by: Karli Reiding

Timo van Duijn, HLO Leiden
March 2013 – July 2013
Monstervoorbewerking van bacteriële cel pellets voor massaspectrometrische analyse van beta-lactamase in antibiotica resistente bacteriën
Supervised by: Paul Hensbergen

Robert Huls, VU Amsterdam, MSc
February 2013 – May 2014
Analysis of urinary NGF using a Proteomics Approach and LC-MS Analysis – A Biomarker for overactive bladder?
Supervised by: Martin Giera

Emmanuel Gay, Univeristy of Montpellier, France, MSc
February 2013 – August 2013
Comprehensive analysis of fatty acids and sterols by GC-MS
Supervised by: Martin Giera

Jordy Hogendijk (ROC Amsterdam)
Sept 2012 – July 2013
New extraction techniques and library project
Supervised by: Suzanne van der Plas-Duivensteijn

Guinevere Kammeijer, VU Amsterdam, Master Anal. Chem.
September 2012 – April 2013
Small scale sample preparation with CE-MS/MS.
Supervised by Anton Heemskerk and Oleg Myboroda

Anouk Botermans (Avans Hogeschool)
Sept 2012 – July 2013
Proteomics of embrionic development of zebrafish
Supervised by: Suzanne van der Plas-Duivensteijn

Marine Lestrade, Faculte des Sciences Foundamentales et Appliquees, Universitee de Pointiers
June 2012 – August 2012
Robust protein abundance estimation by sequence coverage extension
Supervised by: Alex Henneman

Pieter Kooijman, VU Amsterdam
May 2012 – August 2012
Ultra low flow direct infusion analysis

Rudmer Postma, Leiden University
April 2012 – October 2012
NMR-based metabolomic analysis of cerebrospinal fluid in migraine
Supervised by: Axel Meissner and Aswin Verhoeven

Pawel Link-Lenczowski, Jagiellonian University, Poland
16th – 27th of January 2012
Analysis of N-glycosylation features associated with malignancy and metastasis.
Supervised by: Manfred Wuhrer

Wendy Plugge, Hogeschool Leiden
Dec 2011 – April 2012
Expansion of Taverna Workflows for Data Analysis in Proteomics
Supervised by: Magnus Palmblad and Alex Henneman

Hulda Jonasdottir, VU Amsterdam, MSc
September 2011 – June 2012
Lipid Analysis in human synovial fluid of arthritis patients by LC-Ms/MS
Supervised by: Martin Giera

Willem Jonker, VU Amsterdam, MSc
September 2011 – April 2012
FTICRMS based Lipidomics
Supervised by: Martin Giera

Agnes Hipgrave Ederveen, Hogeschool Leiden, Bsc
August 2011-June 2012
Analysis of glycopeptides with reversed phase chromatography and oligosaccharides with HILIC coupled with nanoLC-ESI-MS/MS
Supervised by: Albert Bondt

Ksenia Yashina and Boris Nagaev, Moscow State University
July 2011 – August 2011
Integration of MS-GFDB in peptide/protein identification workflows
Supervised by: Magnus Palmblad

Marie Ciret, University of Poitiers
June 2011 – Aug 2011
Algorithms for constructing and searching peptide spectral libraries in proteomics
Supervised by: Magnus Palmblad and Alex Henneman

Khalid Ahmed, Hogeschool Leiden
April 2011 – June 2011
New sample preparation method for proteome analysis
Supervised by: Oleg Klychnikov

Amir Dadashzadeh, Hogeschool Leiden
May 2011 – August 2011
Additives for enhancing negative electrospray in metabolomics research
Supervised by: Rico Derks and Dick-Paul Kloos

Kevin van der Graaf, Hogeschool Leiden, BSc
April 2011 – July 2011
Optimizing methods for IgG F(ab’)2 N-glycan analysis
Supervised by: Manfred Wuhrer and Albert Bondt

Nienke Derks, Leiden University
March 2011 – June 2011
Detection of CSF peptide changes during the progression of Alzheimer’s disease

Antoinette van Ouwerkerk, Leiden University.
Jan 2011 – July 2011
Analysis of the diagnostic potential of immunoglobuline glycosylation in Lyme Disease
Supervised by: Manfred Wuhrer and Maurice Selman

Kay Schallert,University of Magdeburg
Jan 2011 – July 2011
Development of a workflow for in-depth, quantitative phosphoproteomics
Supervised by: Manfred Wuhrer and Paul Hensbergen

Maja Pucic, University of Zagreb, Croatia
Nov 2010 – Jan 2010
The variability of IgG glycosylation in a Croatian population study
Supervised by: Manfred Wuhrer

Daan Luining, Hogeschool Leiden
Oct 2010 – June 2011
Development of new measurement strategies that enable a rigorous quantitative comparison of multiple patient samples by using isotopically labeled peptides as internal standards.
Supervised by: Liam McDonnel and Rene van Zeijl

Ruben Curfs, Leiden University
Oct 2010 – March 2011
Glycan microarray analysis of anti-carbo-hydrate autoantibody responses in colorectal cancer
Supervised by: Manfred Wuhrer

Marcus Hoffmann, Max Planck Institute Magdeburg
Sept 2010 – March 2011
Tandem Mass Spectrometry of Glycopeptides
Supervised by: Manfred Wuhrer

Artem Artemov, Moscow State University
Aug 2010 – May 2011
Cross-platform analysis of biomarkers and clinical predictors in Urinary Tract Infections

Vladimir Arzhanik and Daria Shalaeva, Moscow State University
Juli 2010 – Aug 2010
Workflows for Peptide Identification by Tandem Mass Spectrometry

Bjorn Victor, Institute of Tropical Medicin in Antwerpen
Juni 2010 – Nov 2011
Molecular Characterization of Excretion-Secretion Products of the Parasite Taenia solium
Supervised by: Magnus Palmblad. Labwork by: Kate Mostovenko and Suzanne van der Plas – Duivesteijn

Alegria Carrasco Pancorbo, University of Granada
Juni 2010 – Okt 2010
MS profiling of olive’s oil polyphenols in human urine

Nico van den Oever and Georgi Kanev, Hogeschool Leiden
May 2010 – June 2010
MALDI imaging mass spectrometry: toward high mass proteins
Supervised by: Liam McDonnell, Renee van Zeijl and Alexandra van Remoortere

Kathrin Stavenhagen, Beuth Hochschule fuer Technik Berlin
March 2010 – August 2010
Glycomics of cancer tissues
Supervised by: Manfred Wuhrer

Lisette Cornelissen, LUMC
March 2010 – June 2010
Regulated patterns of IgG Fc and Fab glycosylation in murine schistosomiasis
Supervised by: Manfred Wuhrer

Matthias Borowiak, University of Magdeburg
March 2010 – June 2010
Cancer-induced changes in the total plasma N-glycome
Supervised by: Manfred Wuhrer

Erik Blok, LUMC
March 2010 – June2010
Natural glycan arrays for analysis autoantibodies in cancer
Supervised by: Manfred Wuhrer

Mahdi Hemayatkar, Pasteur Institute of Iran, Tehran
February 2010 – July 2010
Glycosylation analysis of recombinantly expressed proteins and human plasma proteins
Supervised by: Manfred Wuhrer

Arne vd Meer, VU
Jan 2010 – Sept 2010
Evaluation of a new API source and appliction of the source for the analysis of samples of biological origin
Supervised by: Ralph Schieweck

Erica Gianazza, University of Milano-Bicocca
Jan 2010 – Dec 2010
Biomarker research for renal cell carcinoma

Miguel García, Escuela Politécnica Nacional (Ecuador), bachelor
October 2009 – August 2010
Taenia solium proteomics using ion trap and ultrahigh-resolution time-of-flight mass spectrometry

Elizabeth Minda, Universidad Central del Ecuador
October 2009 – March 2010
Proteomics and molecular diagnostics of Taenia solium

Gillian Lee Hertlein,VU Amsterdam
June 2009 – September 2009
Novel tools for mitochondrial proteomics of cells carrying a mitochondrial DNA mutation
Supervised by: Paul Hensbergen

Anfisa Popova and Kirill Prusov, Moscow State University
June 2009 – July 2009
Peptide Identification by Tandem Mass Spectrometry

Nico de Velde, Hogeschool Leiden
April 2009 – June 2009
Imaging lipids using Fourier transform ion cyclotron resonance mass spectrometry
Supervised by: Liam McDonell

Ivar Lugtenburg and Youri Hoogstrate, Hogeschool Leiden
April 2009 – July 2009
Retention time prediction of amino acid sequences
Supervised by: Magnus Palmblad and Alex Henneman

René Hennig, University of Magdeburg
March – October 2009
Development of a sample preparation method for APTS-labeled N-glycans using HILIC-SPE.
Supervised by: Manfred Wuhrer

Sanne de Jong, LUMC
March 2009 – June 2009
The role of antibody glycosylation in humoral responses to inflenza and tetanus vaccination
Supervised by: Manfred Wuhrer

Jeroen Paardekooper Overman, VU Amsterdam
January 2009 – May 2009
Quantitative proteomic analysis of mitochondria from cells carrying a disease causing tRNA mutation
Supervised by: Paul Hensbergen

Evelyne Steenvoorden, Hogeschool Leiden
October 2008 – September 2009
A high throughput method for glycan analysis of specific proteins
Supervised by: Manfred Wuhrer

Lily David, Hogeschool Leiden
October 2008
Evaluation of a new type of solid-phase extraction micropipette tips

Bo Blanckenburg, TU Delft, master
October 2008 – August 2009
Direct Infusion Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Rapid Screening of Body Fluids

Dick-Paul Kloos, VU Amsterdam
September 2008 – July 2009
Miniaturization of the sample preparation workflow for peptidomics
Supervised by: Rico Derks

Lily David, Gert-Jan den Heijer and Wai Yi Leung, Hogeschool Leiden
September 2008 – January 2009
Comparative Gene and Protein Expression Analysis
Supervised by: Magnus Palmblad and Alex Henneman

Olga Gancharova and Mikhail Kuravskiy, Moscow State University
June 2008 – August 2008
Visualization of Comparative mRNA and Protein Expression Analysis

Kawita Kanhai (LUMC)
maart 2008 – september 2008
Peptide- and protein profiling in body fluids using mass spectrometry-based clinical proteomics