Past meetings

Fall Meeting of the Netherlands Proteomics Platform


22nd January 2018

Congrescentrum 'In De Driehoek' ( | near Utrecht CS)

Willemsplantsoen 1c

3511 LA Utrecht


To register, please send an email to


Program theme: 'Modified proteins and protein variants in health and disease'


09.00 - 09.30           REGISTRATION & COFFEE


09.30 - 09.35           Welcome

Jeroen Demmers (NPP steering committee | Erasmus University Medical Center, Rotterdam)


09.35 - 10.30           KEY NOTE LECTURE | MS-based immunopeptidomics - accelerating the development of cancer immunotherapy

Michal Bassani-Sternberg (Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne)


10.30 - 11.00           Proteogenomic analysis of alternative splicing in cancer

Gosia Komor (NKI & VU University Medical Center, Amsterdam)

11.00 - 11.30           Monitoring the ubiquitinome upon malfunctioning of the proteasome
                                Lennart van der Wal (Erasmus University Medical Center, Rotterdam)


11.30 - 12.00           Proteogenomics data integration to reveal the molecular mechanism of COPD

Peter Horvatovich or Victor Guryev (University of Groningen, Groningen)


12.00 - 13.30           LUNCH | 5-minute vendor pitches starting at 13.00 h


13.30 - 14.00           TBA (PTMs)

                                Leonie Kollenstart (Leiden University Medical Center, Leiden)


14.00 - 14.30           The role of protein synthesis and phosphorylation in synaptic plasticity

Charlotte van Gelder (Utrecht University, Utrecht)


14.30 - 15.00           Open slot for selected talk    



15.00 - 15.30          TEA BREAK


15.30 - 16.00           Data-dependent versus independent MS for comprehensive tumor proteome profiling

Davide Chiasserini (VU University Medical Center, Amsterdam)


16.00 - 17.00           KEY NOTE LECTURE | A proteomic view on cellular signaling and chromatin regulation

Jeroen Krijgsveld (Deutsches Krebsforschungszentrum (DKFZ), Heidelberg)


17.00 - 18.00           CLOSURE & DRINKS




16th Fall Meeting of the Netherlands Proteomics Platform

14 December 2016 -  Auditorium

Vrije Universiteit, Amsterdam



NPP Program

'Next-generation proteomics applications'



9.00-9.30         Registration and coffee


9.30- 9.35        Welcome

Connie Jimenez (NPP steering committee, VUmc)


9.35- 9.45        Update EuPA 

Meike de Wit (NPP representative EuPA Young Proteomics Investigator Club)


9.45-10.15       Drug Resistance Assessed by Multi-Proteomics Approaches

Simone Lemeer, UU, Utrecht


10.15-10.45     HLA-peptidomics, applications in T-cell mediated therapy

                        Peter van Veelen, LUMC, Leiden




10.45-11.45     Proteogenomics of cancer

Bing Zhang, Baylor College of Medicine, Houston, Texas



11.45-13.00     LUNCH BREAK




The 14th Fall Meeting of the Netherlands Proteomics Platform

This year it will be held at the Leiden University Medical Center in Leiden on Friday November 13th 2015.

Registration and submission of abstracts for an oral presentation (max 300 words) can be sent to Please put 'NPP Fall Meeting' in the subject heading. 




9.00-9.40           Registration and coffee


9.40- 9.45          Welcome

Paul Hensbergen (NPP steering committee, LUMC)


9.45-10.10         Synaptic Proteomics using SWATHTM of Rodent versus Primate brain

Nikhil J. Pandya, Vrije University, Amsterdam


10.10-10.35       Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics; method evaluation and application in colon cancer

                        Meike de Wit, VUmc, Amsterdam


10.35-11.00       PhosphoPath: Visualization of Phosphosite-centric Dynamics in Temporal

Molecular Networks

Linsey Raaijmakers, Utrecht University


11.00-11.30       Coffee/tea break


11.30-12.00       Targeting resistance to proteasome inhibitor therapy: a metabolomics approach

                        Celia Berkers, Utrecht University


12.00-12.30       Proteasome malfunctioning and ubiquitinome dynamics

                        Jeroen Demmers, ErasmusMC, Rotterdam


12.30-13.30       LUNCH


Microbial Proteomics


13.30-14.30   Quantitative (phospho)proteomics in analysis of microbial regulatory networks

Dr. B. Macek, Director Proteome Center Tubingen, Germany


14.30-15.00       Coffee break


15.00-15.25       Rapid and strong induction of eEF2 phosphorylation during viral infection

Emmely Treffers, LUMC, Leiden


15.25-15.50       Absolute quantification of proteins in the spores of the pathogenic food spoiler Bacillus cereus

Sacha Stelder, University of Amsterdam


15.50-16.15       Proteomic analyses of (antibiotic resistant) clinical bacterial isolates

Frank Fleurbaaij, LUMC, Leiden


16.15-16.40       Clostridium difficile cell surface proteins involved in the regulation of adhesion

Hans van Leeuwen, LUMC, Leiden


16.40-               Drinks



Fall Meeting of the Netherlands Proteomics Platform
November 14, 2014

Location: Erasmus MC Rotterdam - onderwijscentrum, Prof. Andries Queridozaal (lectures) and Espresso bar (registration, coffee, lunch, sponsors)

Program 'Implications of the draft human proteome and subproteome in health and disease'

9.00-9.40           Registration and coffee


9.40- 9.45          Welcome

Arzu Umar (NPP steering committee, Erasmus MC)


9.45-10.00         Update EuPA, HUPO

Connie Jimenez (NPP steering committee, VUmc)




10.00-11.00     Implications of the human draft proteome in health and disease

Bernhard Kuster (Technical University Munich, Munich, Germany)


11.00-11.30       COFFEE/ TEA BREAK


11.30-12.00       Towards a comprehensive characterization of colorectal cancer-associated glycosylation changes

Stefanie Holst (Leiden University Medical Center, Leiden, The Netherlands)


12.00-12.30       A 4-protein profile predicts tamoxifen treatment outcome in recurrent ER+ breast cancer

Tommaso De Marchi (Erasmus University Medical Center, Rotterdam, The Netherlands)


12.30-13.00       Panel of regulated proteins in serum for diagnostics of cervical cancer and cervical intraepithelial neoplasias and follow-up treatment

Alexander Boichenko (University of Groningen, Groningen, The Netherlands)


13.00-14.00       LUNCH


14.00-14.30       De Novo discovery of phenotypic intra-tumor heterogeneity using IMS

Benjamin Balluff (Leiden University Medical Center, Leiden, The Netherlands)


14.30-15.00       Transfer of regulatory protein networks via extracellular vesicles as a possible mechanism of mediating apoptosis-resistance

A. Wojtuszkiewicz (VU University Medical Center, Amsterdam, The Netherlands)


15.00-15.30       Changes in the human hippocampal proteome during Alzheimer’s disease

Saskia van der Vies (VU University Medical Center, Amsterdam, The Netherlands)


15.30-16.00       COFFEE/ TEA BREAK



16.00-17.00       PTMs in the human brain

Martin Larsen (University of Southern Denmark, Odense, Denmark)


17.00-18.00       DRINKS


13th NPP Fall meeting

8 November 2013, VUmc, Amsterdam

Proteomics suite of applications and new developments

9.00-9.30         Registration and coffee


9.30- 9.45        Welcome, update EuPA, HUPO

Connie Jimenez (NPP steering committee, VUmc)


9.45-10.15       Next generation proteomics: an integrative transcriptome and proteome study of rat tissues from different genetic backgrounds

Teck Yew Low, Utrecht University, Utrecht


10.15-10.45     AMPA receptor interactome: Identification of true protein-protein interactions

Nikhil Pandya, Vrije Universiteit, Amsterdam


10.45-11.15     COFFEE/ TEA BREAK


11.15-11.45     Quantitative protemics, to label or not to label?

NQ Liu, Erasmus Medical Center, Rotterdam


11.45-12.15     Disease-related N-glycoproteome of Arabidopsis infected by downy mildew

                        Dmitry Lapin, Plant-Microbe Interactions group, Utrecht University


12.15-12.45     Protein biomarkers for cervical cancer: from shotgun to targeted MS quantification

Alexander Boichenko, University of Groningen, Groningen


12.45-13.45     LUNCH


13.45-14.15     Label-free phosphoproteomics of cancer cells

Sander Piersma, VU University Medical Center, Amsterdam


14.15-14.45     A novel secreted metalloprotease from Clostridium difficile cleaves cell surface LPXTG-proteins involved in adhesion

Paul Hensbergen, LUMC, Leiden



14.45-15.45     New developments in targeted mass spectrometry: from MRM to PRM and SWATH to antibody-based analyses

Jan van Oostrum, CRP-Santé and Luxembourg University, Luxembourg



15.45-16.45     Proteogenomic analysis of TCGA colorectal carcinomas

Robbert Slebos, Vanderbilt University, Nashville, USA


16.45-18.00     DRINKS


To register, please send an email to Dr. Connie Jimenez:

Fall Meeting Netherlands Proteomics Platform 


30 Nov. 2012, De Rijn, VU University Medical Center, Amsterdam 

To register, send an email to



'Current state-of-the-art of Proteomics in the Netherlands'

9.00-9.30         Registration and coffee


9.30- 9.45        Welcome, update EuPA, HUPO

Connie Jimenez (NPP steering committee, VUmc)


9.45-10.00       Update on the HUPO chromosome project

Peter Horvatovich, University of Groningen, Groningen


10.00-10.30     Lung cancer proteomics

Tieneke Schaaij-Visser, VU University Medical Center, Amsterdam


10.30-11.00     A proteomic approach to study proteasome dysfunctioning

Karin Sap, Erasmus Medical Center, Rotterdam


11.00-11.30     COFFEE/ TEA BREAK


11.30-12.00     Labeled and unlabeled approaches in cardiovascular proteomics

Arjen Scholten, Utrecht University, Utrecht


12.00-12.30     Identification of a prognostic protein profile for triple negative breast cancer

Arzu Umar, Erasmus Medical Center, Rotterdam


12.30-13.00     Targeted proteomics in energy metabolism and ageing

Karin Wolters, University of Groningen, Groningen


13.00-13.30     LUNCH


13.30-14.00     Mass Spectrometry and Molecular Phylogenetics

Magnus Palmblad, Leiden University Medical Center, Leiden


14.00-14.30     Frog skin secretion peptidomics

Martijn Pinkse, Delft


15.00-15.30     COFFEE/ TEA BREAK


15.30-16.00     Quantitative mass spectrometry-based proteomics for epigenetics

Michiel Vermeulen, University Medical Center Utrecht, Utrecht





16.00-17.00     New developments in bioinformatics for mass spectrometry-based proteomics

Eric Deutsch, Institute for Systems Biology, Seattle, USA


17.00-18.00     DRINKS

28 okt. 2011, Utrecht, joint Fall meeting Netherlands Proteomics Platform and NVBMB

Oct 15, 2010, Fall Meeting Netherlands Proteomics Platform
Topic Targeted proteomics using multiple reaction monitoring

Oct 15, 2010, Fall Meeting Netherlands Proteomics Platform

Topic Targeted proteomics using multiple reaction monitoring. Program
Location: Uithof in Utrecht. Routedescription
Slots open for orals (all topics)!
To attend or present, please send an email to Dr. Monique Slijper ( )

NPP Voorjaarsmeting, 11 april 2008, VUMC Amsterdam,

Lecture Hall De Maas Morning Workshop ‘Mining of proteomics data: From discovery towards biological insight’ Contributions on Bioinformatics tools including Cytoscape and Ingenuity. Please sign up by sending an email to
NB In the afternoon of April 11 there is a separate proteomics symposium hosted by VUmc and Applied Biosystems: please see

Programme download programme

09.30-10.30      Registration and coffee

10.30-10.35      Welcome
                         Connie Jimenez (NPP steering committee)

10.35-11.00      Overview strategies for mining proteomics data
                         Connie Jimenez, OncoProteomics Laboratory, VUmc

11.00-12.00      Building Disease Models from Transcriptomic, Proteomic and Metabolomic Data- Ingenuity demo
                         Adam Corner, Ingenuity Systems
12.00-13.00      LUNCH

13.00-14.00      'Pathway analysis in cancer'- Cytoscape demo
                         Rogier Versteeg, AMC

Amsterdam NPP Workshop End

14.00-17.00      Mini-symposium ‘From Discovery through Validation towards Biological Insight’ co-organized by VUmc & Applied Biosystems (see for program)

Meetings organized by the proteomics platform

'Pushing the Limits of detection in Proteomics'
Friday Nov 30, 9.00-17.30
VU University Medical Center, Amsterdam

The program will be a combination of oral presentations of our Platform members, complemented with two keynote lecturers. download programme
PRESENTATION: If you also would like to present your results in an oral presentation, please send an abstract by reply mail ASAP (not later than Nov9). Unfortunately there will be no space for posters.
REGISTRATION: Please register before november 20 by reply mail and include your contact details. As for the registration fee, this will be at maximum  Eur 20,- We request that you are (or become) a member of the NVBMB, our mother society .

Programma Voorjaarsbijeenkomst KNCV, 19 april de Reehorst, Ede

Sessie NPP Comparison of software tools for label-free LC-MS quantitation

9.30-10.00    Twan America (PRI, Wageningen): Introduction comparative LC-MS
10.00-10.20  Wilfried Voorhorst (Thermo Scientific): SIEVE
10.20-10.40  Hans Vissers (Waters): ProteinLynx Global Server
10.40-11.00  Axel Parbel (GE Healthcare): DeCyderMS
11.00-11.20  Marius Codrea (VU, Amsterdam): MZMine+ home-made alignment algoritm
11.20-11.40  Thang Pham (VUmc, Amsterdam): MSInspect & PEPPeR
11.40-12.00  General discussion

Plenaire sessie NPP/NVBMB
Proteomics: overview and current status

14.30-15.00   Monique Slijper (Utrecht University): Differential proteome analysis
15.00-15.30   Prof. A.M. Deelder (LUMC, Leiden): Clinical proteomics
15.30-16.00   Alain van Gool (Organon, Oss): Proteomics in Pharmaceutical Industry
16.00-16.30   Gerco Angenent (PRI, Wageningen): Protein-protein complexes
16.30-16.45   Discussion

13 Oct. 2006, LUMC, Leiden:
Fall meeting 2006 of the Netherlands Proteomics Platform
Hot topics in proteomics: quantification and phosphorylation

5 Oct. 2005:
Fall meeting 2005 of the Netherlands Proteomics Platform programme

4 Oct. 2004:
Fall Meeting Netherlands Proteomics Platform, Biomarker Discovery in the post-genome era, program & abstracts posters

15 Apr. 2004:
Data-mining, KNCV Vereningendag, Reehorst, Ede, program

1 Oct. 2003:
Phosphoproteomics & Novel developments in proteomics technology, Reehorst, Ede, program & abstracts posters

15 Nov. 2002, From classical to innovative proteomics Uithof, Utrecht

15 Apr. 2002, workshop 'the Ins and Outs of 2D-Image Analysis', Plant Research Int., Wageningen

12 Okt. 2001, symposium 'Proteomics in Practice, Universiteit van Leiden

8 Feb. 2001 kick-off meeting, Vrije Universiteit, Amsterdam. See abstracts of proteome research in the Netherlands