Members

Catarina Marques

Ph.D. student

Ayse Erözenci

Ph.D. student

Berend Gagestein

Mass spectrometry

Andrea Valles

PhD student

Valentina Cordo

PhD student

Iris Glykofridis

PhD student

Frank Rolfs, Ph.D.

Post-doc

Giulia Mantini, Ph.D.

Giulia worked on multi-omics integration of pancreatic cancer.

Sanne Martens de Kemp, Ph.D.

Sanne works on a KWF-sponsored project in collaboration with the NKI (Dr. Beatriz Carvalho and Prof. Gerrit Meijer) entitled “Signaling pathways in colorectal adenoma to carcinoma progression”. To this end, phosphoproteome profiling will be employed to study patient tissues as well as organoids. In functional studies candidate oncogenic drivers will be assessed.

Malgorzata Komor, M.Sc., Ph.D. student

Malgorzata Komor received a BSc in Bioinformatics and Systems Biology at Warsaw University in Poland in 2012 and a MSc in Bioinformatics and Systems Biology at Vrije Universiteit Amsterdam in 2014. Her PhD project is a joined effort of Oncoproteomics Lab and Tumour Profiling Unit of the VU medical center. Its aim is to identify tumour-specific protein biomarkers for early detection of colorectal cancers. Currently her main interest is proteogenomics.

Tessa Le Large, M.Sc., Ph.D. student

Tessa Le Large joined the OPL as a PhD student in September 2014. She studied Medicine until December 2013 at the VU and worked as a medical doctor at the department of Surgery in the VU Medical Center until August 2014. With a special interest in Oncology she currently works as a PhD student on Phosphoproteomics for therapy response prediction in pancreatic cancer. This is a joint project of VUmc and AMC.

Robin Beekhof, M.Sc., Ph.D. student

Robin Beekhof joined the OPL as a PhD student in September 2014. He studied biomedical sciences as a bachelor (VU) and finished his master in Oncology in 2013 (VUmc). His main research interest is the phosphoproteome in colorectal cancer. Furthermore, his focus is on characterization, signaling pathways and kinome profiling.

Carolien van Alphen, M.Sc., Ph.D. student

Carolien van Alphen obtained an MSc in Biomedical Sciences at the VU University in Amsterdam. During her internship at the Oncoproteomics Laboratory she worked on the project “Proteomics of an HPV progression model”. Currently she is a PhD student working on a phosphoproteomics project in Acute Myeloid Leukemia (AML). The goal of this project is to determine phosphorylation profiles which will help to personalize treatment of AML patients with kinase inhibitors. This research is a joined project with the Department of Hematology of the VU Medical Center

Ing. Tim Schelfhorst, B.Sc.

Tim is a research technician who joined the OPL in February 2015 after completing his HLO internship. He supports expression profiling projects and explores the application of highthroughput extracellular vesicle methods to the analysis of biofluids.

Koen van der Mijn, M.Sc., VUmc Dept. Medical Oncology

Topic: Patient selection for targeted therapy using exosome proteomics and phosphoproteomics

Marta Del Campo Milan, Ph.D.

Marta got her bachelor’s degree in Biology and master’s degree in Biotechnology at the Universidad Autonoma de Madrid (Spain). She started her PhD at VUmc in September 2010 in the Clinical Chemistry department in collaboration with the OncoProteomics Lab. Her PhD forms part of the European Neuroscience Campus (ENC) Network within the Erasmus Mundus Joint Doctorate program. The goal of this PhD project is the validation of biomarkers in CSF for early diagnosis of Alzheimer’s disease using antibody-based approaches. The biomarker candidates that are currently being pursued were discovered by the OPL in the EU kp6 cNeuPRO project.

Joey Lam, M.Sc., Ph.D. student

Topic: breast cancer proteomics in the context of the ATX trial.

Inge de Reus, B.Sc.

Inge is a research technician at the OPL, She joined the OPL in 2007 after completing her HLO internship at the same laboratory. The focus in 2007-2009 was on making kinobeads to allow for global kinome proteomics (in collaboration with the Dept. Med. Chemistry, VU) and on implementing TiOx-based strategies for phosphopeptide capture and phosphoproteomics. After one year of leave, she returned to the OPL in 2011. Currently she works together with Dr. Tieneke Schaaij-Visser on validation of lung cancer biomarkers in sputum, in collaboration with Prof. Egbert Smit, Dept. Pulmonology.

Marc Warmoes, M.Sc., Ph.D. student

Marc has an MSc in Biotechnology and Bioinformatics. His main aim is the identification of biomarkers for diagnostic and predictive use in breast cancer. He uses mouse models of Brca1 (-deficient) breast cancer with high similarity to human BRCA1-mutated breast cancer. Markers predictive for treatment are identified by treating mice with the drug of interest. He worked previously at Agendia, a company that brought an FDA-approved multivariate diagnostic test (microarray) for breast cancer from the research bench to the clinic. In recent years, he has gained a strong interest in cancer cell metabolism, an area of research hopes to pursue in the future.

Gideon Oudgenoeg, Ph.D.

Dr Gideon Oudgenoeg joined the OPL in September 2010 to develop quantitative methods for biomarker discovery in stool, mainly using MRM. Gideon has an MSc in biochemistry and organic chemistry from the University of Amsterdam (1999) and obtained his PhD in Biochemistry and Food Chemistry at Wageningen University (2004) on enzymatic cross-linking of proteins and carbohydrates. Subsequently he joined the laboratory of the Government Chemist in Teddington, UK as a researcher Mass Spectrometry where he was responsible for intact protein analysis within a DTI-funded project by an industrial consortium of pharmaceutical companies, determining host cell proteins in complex mixtures. After two years at LGC, he headed the metabolite profiling group at the University of York in York, UK, within a project from the Bill & Melinda Gates foundation, responsible for high-throughput analysis of the anti-malarial drug Artemisinin in Artemisa annua, using a UPLC-Orbitrap platform. After returning to the Netherlands in 2007, Gideon has worked in the Biomolecular mass spectrometry and Proteomics group of Albert Heck at Utrecht University, focusing on quantitative phosphorylation of the yeast mediator complex by LCMS methods (Orbitrap/FT) and methylation of yeast histones by targeted MS methods (MRM) in close collaboration with the Netherlands Cancer Institute (NKI-AVL), before joining the OPL.

Tieneke B.M. Schaaij-Visser, Ph.D.

Tieneke got a bachelor’s degree in Biomedical Sciences and a master’s degree in Oncology at the Vrije Universiteit in Amsterdam. She did her PhD at the Biomolecular Mass Spectrometry and Proteomics Group of Utrecht University in collaboration with the Tumor Biology Section of the Otolaryngology/Head and Neck Surgery department at the VU University Medical Center. During this project, she used 2D-DIGE to study the proteomes of squamous cell models and head and neck cancer patient tissues and discovered biomarkers for the early detection of head and neck cancer. Tieneke started as a postdoc at the OPL in 2009, and her project is embedded in the multi-centered CTMM-AIR FORCE project. The aim is to discover new protein biomarkers for lung cancer as well as head and neck cancer using genetic mouse models and targeted proteomics approaches.

Silvina Fratantoni, Ph.D.

Silvina worked as a Ph.D.-level research technician at the OncoProteomics Laboratory. Her research focused on biomarker discovery in cerebrospinal fluid from Alzheimer’s disease patients using mass spectrometry-based techniques.

Marleen Koel-Simmelink, Ph.D.

Marleen worked part-time as a Ph.D.-level research technician at the OncoProteomics Laboratory, and part-time at the Dept. of Molecular and Cellular Biology and Immunology (collaboration Dr. CE. Teunissen). Her research focus is multiple sclerosis and biomarker discovery in cerebrospinal fluid. At the Dept. of MCBI she has been setting up a Luminex-based system for (candidate) biomarker validation.

Jakob Albrethsen, Ph.D.

Jakob Albrethsen got his masters in protein biochemistry at the University of Copenhagen (Denmark) in 2001. He got his PhD in 2006 at the same university in collaboration with the Glostrup University Hospital (Denmark) on proteomics of colorectal cancer tumors and serum. His research into clinical proteomics was continued in 2007 by a one-year project at the OPL dedicated to the examination of nuclear sub-fractions of colorectal cancer tissue using state-of-the-art proteomics equipment at the OPL.

Uros Rajcevic, Ph.D.

Uros, a postdoc hailing from the NorLux Neuro-Oncology Laboratory, CRP-Sante (Luxemburg) and working in the context of the EU kp6 AngioTargeting project, spent 1 year at the OPL for iTRAQ-based proteomics in a sophisticated rat xenograft model for glioblastoma multiforme (GBM).

Zineb El Filali, M.Sc.

Zineb worked as a research technician at the OPL and pioneered the OPL protocol for serum profiling using Dynabeads and MALDI-TOF MS.

2026- Matthijs Biesma, Internship Master Oncologie, Amsterdam UMC
Project: “Plasma (extracellular vesicle) proteomics for biomarker discovery in pancreatic cancer”

2026- Ada Nushi, Internship Master Oncologie, Amsterdam UMC
Project: “Cerebrospinal fluid (extracellular vesicle) proteomics for biomarker discovery in dementia”

2026- Nora Krajinovic, Internship Master Oncologie, Amsterdam UMC
Project: “Plasma derived extracellular vesicle proteomics for biomarker discovery in ovarian cancer”
2026- Risheet Lal, literature thesis Biomedical sciences, LUMC
Thesis: “Organ proteins in plasma as disease biomarkers”

Luke Pattiwael, Internship Master Biomolecular Sciences, VU

Project: Proteomics of extracellular vesicles for biomarker discovery in renal cancer

Risheet Lai, Internship Master Biomolecular Sciences, VU

Project: Plasma (extracellular vesicle) proteomics for biomarker discovery in ovarian cancer

2025 Irene Blasquez Garcia, visiting PhD student from Molecular Bioscience Doctoral Program at the Universidad Autónoma de Madrid, Spain

Project: Low level proteomics of immune subset isolated from plasma

2025 Raquel Rejas, visiting PhD student from the Functional Proteomics Unit at the Instituto de Salud Carlos III in Madrid, Spain

Project: Phosphoproteomics of isogenic models of colorectal cancer

2025- Beyza Betül Bahadır, visiting Erasmus student 

2024 Anna D’Antuono, visiting PhD student from the University of Parma, Italy

Project: Indivdualized therapy selection based on tALL phosphoproteomics

2024 Giuliana de la Rosa, University of Naples, Italy

Project: CSF proteomics in multiple sclerosis

2024- Vera van der Wal Stalidzane, internship student Master Biomedical Sciences UvA

Project: Exploring the extracellular vesicle proteome in relation to BRAF V600E mutation in CRC cell lines

2024- Liva Stalidzane, internship student Master Biomolecular Sciences VU

Project: Exploration of perchloric acid precipitation as plasma sample preparation method for high-throughput proteomic profiling

2023 – Felix Zwolle, internship student Bachelor Biomedical Sciences VU

Project: Investigation of secretion pathways of stress granules in colorectal cancer

2023 – Adinda Kuhr, internship student master Oncology Amsterdam UMC

Project: Targeting the secretory pathway in cancer cells

2023- Clara Puhlen, internship student master Bioinformatics VU

Project: Bioinformatic exploration of the plasma proteome in diet and lifestyle related diseases

2022 – Elena Navarro-Carrasco, guest PhD student from the University of Salamanca with EMBO Scientific Exchange Grants

Project: VRK1 function and targets in the epigenetic chromatin remodelling during the DNA damage response

2022 – Nicole Hogervorst, internship student master Oncology Amsterdam UMC

Project: Cancer secretome in relation to classical secretion inhibition and BRAF status

2022 – Maarten van Kempen, internship student master Oncology Amsterdam UMC

Project: Functional analysis of pathways implicated in altered protein secretion in cancer

2022 – Fatma Kaya, internship bachelor Biomedical Sciences VU

Project: Cancer secretome in relation to autophagy inhibition

2022 – Ilse de Ruiter, internship bachelor Biomedical Sciences VU

Project: Streamlining sample preparation of urinary extracellular vesicles for clinical proteomics

2021 – Elysia Yau, internship student master Pharmaceutical Sciences VU

Project: Analysis of the anti-cancer effects of high dose vitamin C on the cancer proteome and phosphoproteome 

2021 – Tugce Su Cobanoglu, internship student master Bioinformatics VU

Project: Kinase substrate relation prediction for precision medicine in individual cancer patients

2021 – Elisa Suarez Martinez, guest PhD student from the University of Sevilla

Project: Proteomics to unravel tumorigenic functions of two related genes. 

2021 – Lorenzo Signorini guest PhD student from Tel Aviv University, Israel, visiting for 3 months in the context of the EU ITN Secret

Project: Advanced bioinformatics to study the cancer secretome. 

Elena Gutierrez Galindo, guest PhD student from University of Stuttgart visiting for 3 months in the context of the EU ITN Secret (2021)

Project: Stiffness-dependent activation of PKD3 and its effect on Golgi-controlled signalling and secretion in cancer cells. 

Merih Ozerin, guest PhD student from University of Stuttgart visiting for 3 months in the context of the EU ITN Secret (2021)

Project: Characterization of the breast epithelial cell proteome and secretome upon transient DLC1 knockdown in the absence or presence of TGFb 

Alexia Gali, guest PhD student from Protatonce, Greece, visiting for 3 months in the context of the EU ITN Secret (2021)

Project: Secretome analysis following treatment with a PKD3 inhibitor 

Noah Dekker, internship student bachelor Biomedical Sciences VU (2021)

Title project: Biofluid exosome proteomics to spearhead non-invasive diagnostics of disease

Loraine Cahn, literature thesis student VUmc School of Medical Sciences

Title: High-dose intravenous vitamin C in the treatment of cancer

Loraine Cahn, literature thesis, Master Oncology, Amsterdam UMC

Title: Synergy of high-dose vitamin C with chemotherapy and immunotherapy

Manuela van Diest, Literature thesis, UvA

Title: The Biogenesis of (Unconventional) Secretory Pathways as a Potential Anti-Cancer Target

Sanne Massaar (2020), literature thesis student master oncology

Title: Malignant functions and therapeutic potential of the cancer extracellular vesicle secretory pathways

Jim Termeulen (2020) Internship master student Bioinformatics, VU University

Title project: Statistical analysis of DIA mass spectrometry data

Lian Wang (2020) Internship master student Biomedical Sciences, Leiden University.

Title project: “Proteomics and phosphoproteomics of cancer extracellular vesicles”.

Khadija Tejjani

Internship student HLO In Holland, title project: Effect of high dose vitamin C in a prostate cancer panel in vitro and correlation to the proteome.

Guillermo Guerrero

Internship master student Bioinformatics and System biology. Title project: “Mousification” of INKA.

Madiha Mumtaz, guest PhD student from University of the Punjab visiting for 6 months.

Project: Identification of Protein markers in Oral Squamous Cell Carcinoma (OSCC).

Fenna Feenstra, Master Oncology internship student

Title project: surface proteome of (prostate) cancer-specific extracellular vesicles

Loes Meijs, Master Oncology internship student

Title project:Proteome-based exploration of markers for cisplatin response prediction and potential synergism with high dose vitamin C treatment in lung cancer focus Small Cell LC

Sughandi Sharma, Master Oncology internship student

Title project:Proteome-based exploration of markers for cisplatin response prediction and potential synergism with high dose vitamin C treatment in lung cancer, focus NSCLC

Yasmin Heirouch  HLO internship student

Yasmin is an internship student from the Hogeschool InHolland. Under daily supervision of Drs. Andrea Valles she works on a project entitled “Vitamin C plasma assay and proteome analysis of anti-cancer vitamin effects”.

Efe Kaya, HLO internship student

Efe is an internship student from the Hogeschool InHolland. Under supervision of Dr. Irene Bijnsdorp and Drs. Ayse Erozenski he works on a project entitled “Urine pan-cancer exosomal proteome” .

Justin van der Woude, HLO Internship

Justin is an internship student from the Hogeschool InHolland. Under supervision of Dr. Davide Chiasserini he works on a project entitled “Evaluation of the peptide-affinity method for isolation of extracellular vesicles from CSF”.

Laura Lorenzo Sanz, visiting PhD student

Laura is a PhD student visiting from Institut d’Investigació Biomèdica de Bellvtige, IDIBELL in Barcelona, Spain. She is supported by a short term EMBO fellowship. Title project: IDENTIFICATION OF SIGNALING PATHWAYS REGULATING CANCER STEM-LIKE CELL PLASTICITY AND SKIN CARCINOMA PROGRESSION

Dr. Mitra Asgharian Rezaee, visiting scientist

Mitra is a visiting scientist from the Kerman University of Medical
Sciences, Kerman, Iran. At the OPL, during her 6 month visit she works
on selected tumor types in the The Cancer Proteome Atlas project.

Paula González Alonso, visiting PhD student from the Autonomous University of Madrid (UAM), Madrid (Spain)

Topic: Phosphoproteomics to identify mechanisms of trastuzumab resistance in Her2 amplified breast cancer

Shuang Wu, visiting clinician of the Department of Gastroenterology and Endoscopy Center, the First Hospital of Jilin University, Changchun China in the context of the Sino-Dutch Bilateral Exchange Scholarship programme

Topic: Colorectal cancer secretome/vesicle proteomics for biomarker discovery

Mark Luinenburg, Master Oncology student, internship

Phosphorylation state of proteins in exosomes derived from GBM and cell lines: a possible biomarker and biological implications

Beatriz Escudero Paniagua, in 2016 visiting PhD student from the Biological Research Center (Centro de Investigaciones Biológicas – CIB Madrid)

Topic: Colorectal cancer proteomics with a focus on the secretome biomarker discovery

Sheree Hazelaar, Master bioinformatics student, internship

Exploring non-negative matrix factorization as a suitable tool to discriminate tumor heterogeneity in colorectal cancer proteomics data

Luuk Hüttig, bioinformatics, internship

Enabling multi-omics data exploration by integrating mass spectrometry-based proteomics data into the genomics database cBioPortal

Olga Maxouri, Master oncology student, internship

Testing of a novel extracellular vesicle isolation method for protein biomarker discovery in urine of prostate cancer patients

Rosita Paleckyte, Master biomolecular sciences VU, internship

Platelet proteomics in pancreatic cancer, exploration of diagnostic potential of single shot nanoLC-MS/MS-based proteomics

Cico Zhang, master bioinformatics student, internship

Pinpointing driver kinases in phosphoproteomics data to uncover the tumor’s Achilles heel for drug targeting

Kimberley Ober, master oncology student, internship

Proteomics of prostate cancer exosomes derived from cell lines and human (prostate cancer patients’) urine samples

Aarzo Kardar, HLO student, internship

Implementation and testing of a novel extracellular vesicle isolation method to urine of prostate cancer patients: method evaluation and assessment of biomarker potential

Erik Meijer, master oncology student, internship

Topic: Proteomics of colorectal cancer tissues in relation to chemotherapy treatment

Roos Kleinendorst, master oncology student, internship

Literature thesis title: Current status of phosphoproteomics for (pre)cllinical applications

Evan Henneberry, master bioinformatics student, internship

Pinpointing driver kinases in phosphoproteomics data to uncover the tumor’s achilles heel for drug targeting

Annalisa Carli, master Biomolecular sciences student, internship

Phosphoproteomics to uncover feedback loops in cancer cells resistant to kinase inhibitors

Logan Bishop-Currey, Master’s Biochemistry and Metabolic Disease student, internship

Exosome proteomics: towards a non-invasive protein biomarker-based assay

Ozlem Senol, M.Sc., research scholar

Visiting scientist who worked at the OPL on a meningioma project in a collaboration with the Department of Neurology, Neurogenetics Unit, Massachusetts General Hospital, Harvard Medical School (USA).

Garcia de Durango Caveda, Cira, Ph.D. student

Cira is a Pharmacist with a degree in Complutense University of Madrid. Currently she is a PhD student from San Pablo CEU University, Madrid, the same University from which she obtained her Master in Molecular Medicine. Her project is about biomarker discovery in Colorectal Cancer and belongs to a Spanish-government founded project named: Deteccion de biomarcadores de diatesis prometastasica en el higado y el tumor primario de pacientes con cancer gastrointestinal, “prometastatic diathesis biomarker detection in liver and in primary tumor in gastrointestinal camcer patients”.

Niek de Klein, master student Bioinformatics, internship

Topic: Statistical modeling of MS/MS peaks

Sushen Adhin, master student Bioinformatics, internship

Topic: Exploring spectral library search for mass spectrometry-based proteomics

Valerie Dusseldorp, master student Oncology, internship

Topic: Proteomics of colorectal cancer exosomes derived from cell lines and human tissue proximal fluids

Hulya Ozturk, master student Oncology, internship

Topic: Proteomics of exosomes of colon cancer cell lines and mouse proximal fluids

Sofia Koustoulidou, master student Oncology, internship

Topic: Proteomics of FFPE material of colon adenomas and carcinomas

Richard Jaarsveld, master student Oncology, internship

Topic: Exosome proteins and their link with cell surface markers for colon cancer

Marjolein Weerts, VU student, thesis

Topic: Cancer exosomes, a survival mechanism.

Barath Kumar, master student Oncology

Topic: Phosphoproteomics of a panel of colon cancer cell lines

Wina Verlaat, master student Oncology, thesis

Topic: Analysis of protein-protein interaction networks integrated with proteomics to identify new cancer genes.

Carolien van Alphen, master student Oncology

Topic: Proteomics of an HPV progression model.

Mehrdad Lavaei, M.D., M.Sc. , master student Oncology

Our longest-staying student: 2008-2010. Mehrdad pioneered our proteomics studies of cancer cell exosomes.

Burcin Colak, bachelor student Medicine VU

Topic: Sputum proteomics to identify lung cancer biomarkers.

Leticia Leon, Ph.D. , master student Bioinformatics, VU

Topic: Network-based analysis of proteomics data.

Frank Neezen , master student Bioinformatics, VU

Topic: Workflows for pathway analysis tools.

Jelmer Nicolai, bachelor student Medicine VU

Topic: Immunohistochemistry of candidate meningioma markers.

Katarzyna (Kasia) Wojcik, Ph.D., internship to get acquainted with proteomics

Topic: Proteomics of PARP-treated Brca1-deficient and proficient mouse breast cancer cell lines

Dewi Wulandari, M.D., master’s student Oncology

Topic: Validation of secretome markers for colon cancer screening using immunological methods.

Huub Kant, M.Sc., master’s student Oncology

Topic: secretome proteomics of fresh human colon cancer resection material to identify biomarkers for non-invasive screening.

Maral Pourghiasian, master student Oncology

Maral worked in the OPL during a 6-month internship on a very successful project “A proteomics based search of plasma markers for colon cancer in tumor secretomes”, using a mouse model. This work has recently resulted in a publication entitled: Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer (Clin Cancer Res. 2012 Feb 20).

Benjamin Emmink, bachelor student Medicine, UMCU

Benjamin has been working at the OPL on a colorectal stem cell project in collaboration with Dr. Onno Kranenburg at the Department of Surgery of University Medical Center Utrecht. This work has resulted in a publication entitled “Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target” (Mol Cell Proteomics. 2011 Dec;10(12):M111.011353).

Muhammed Kapci, bachelor student Molecular Sciences, VU

Topic: platelet proteomics. This work has resulted in a publication entitled “Proteomics of the TRAP-induced platelet releasate” (J Proteomics. 2009 Feb 15;72(1):91-109).

Ann Cathrine Kroksveen, M.Sc.

Visiting Ph.D. student from the University of Bergen (Norway). The aim of her visit was to get familiar with CSF proteomics.

Anne Kjergaard Callesen, M.Sc.

Visiting Ph.D. student from the University of Southern Denmark, Odense (Denmark). The aim of her visit was to get familiar with tumor tissue-based proteomics.