Next generation nanoLC-MS/MS-based proteomics on high-resolution, high-speed mass spectrometry platforms allows for unbiased profiling of protein (variant) expression, and may substantially expand our ability to understand the association between cancer-related genomic variation and cancer phenotypes.


The current infrastructure consists of 3 nano-liquid chromatografy systems on-line coupled to tandem mass spectrometers (see figure proteomics infrastructure):

  • 3 Orbitrap platforms (2x QExactive and 1x QExactive HF, all ThermoFisher)

Tandem mass spectrometers at the OPL (CCA 1-47). Left: next generation Orbitrap, the QExactive (ThermoFisher) (one of the systems is shown). Right: nanoLC system (Ultimate3000) coupled to a QTrap 5500 platform (Applied Biosystems).

IT Infrastructure

After shot-gun data acquisition by nanoLC-MS/MS, raw data are processed by the software tool MaxQuant for peptide/protein identification and quantification. For DIA-MS data we use Spectronaut in conjunction with dedicated libraries.
Data exports to Excel are used for further dedicated statistical analyses, which is also facilitated by the OPL.

The computer infrastructure to cope with the large data flows is regularly upgraded. Currently, computing servers with a total of about 100 cores are connected to the tandem MS data acquisition PCs for fast data processing. Storage servers provide hundreds of TB of local, temporary storage. These servers are connected to the VUmc store4ever system for long term archive, as well as VUmc GreenQloud and the national computing grid for additional computing power.

Forms & Protocols

OPL protocols available upon request

Video instructions

Watch Instruction video FFPE proteomics (English) on Vimeo:

Watch cutting bones 2018 on Vimeo:

Watch video biobank (short) on Vimeo:

Watch video biobank (long) on Vimeo:

Web tool

Please cite the following papers when using the tool:

Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR. INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol. 2019 Apr 12;15(4):e8250. doi: 10.15252/msb.20188250. PubMed PMID: 30979792; PubMed Central PMCID: PMC6461034.


Please cite the following papers when using our tests:
Pham TV, Jimenez CR. Simulated linear test applied to quantitative proteomics. Bioinformatics. 2016 Sep 1;32(17):i702-i709.
Pham TV, Jimenez CR. An accurate paired sample test for count data. Bioinformatics. 2012 Sep 15;28(18):i596-i602.
Pham TV, Piersma SR, Warmoes M, Jimenez CR. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics. 2010 Feb 1;26(3):363-9.


The OPL organizes every year an optional VUmc master course entitled: ‘Biomedical Proteomics’ of 2 weeks that runs end of January-early February.
It encompasses one week of theory (lectures) and one week of practical work as well as hands-on training in data analysis.

It is intended for VUmc master students and our collaborators who wish to obtain more in-depth knowledge of proteomics. Collaborators often bring their own sample for a pilot analysis.

Click here for an impression of the 2018 course


 2019 Schedule Optional Master “Biomedical Proteomics" ; M_CPROTBI09
Theme 1 Proteomics, Mass Spectrometry and Biomedical Applications Coordinator: CR Jiménez
Week/day/date duration Staff Form Subject Room
2 Mon 7-Jan 9.30-10.30 CRJ L Introduction to Proteomics CCA 1.06
2 Mon 7-Jan 10.30-11.30 CRJ L Proteomics to obtain biological insight CCA 1.06
2 Mon 8-Jan 11.30-17.00 n/a Zelfstudie Literature reading n/a
2 Tue 8-Jan 9.30-10.30 CRJ L Proteomics in biomarker discovery To be determined
2 Tue 8-Jan 10.30-11.30 SP L Mass spectrometry in Proteomics CCA 1.06
2 Tue 8-Jan 11.30-12.30 SP L/ Demo Protein identification by Database searching CCA 1.06
2 Tue 8-Jan 12.30-17.00 n/a Zelfstudie Literature reading n/a
2 Wedn 9-Jan 9.00-10.00 DK L Proteomics in cardiovascular research To be determined
2 Wedn 9-Jan 10.00-11.00 DK L Analysis of post-translational modifications To be determined
2 Wedn 9-Jan 11.00-17.00 n/a Zelfstudie Literature reading n/a
2 Thu 10-Jan 9.30-10.30 SP L Quantitative proteomics CCA 1.34
2 Thu 10-Jan 10.30-11.30 CRJ L Phosphoproteomics CCA 1.34
2 Thu 10-Jan 11.30-17.00 n/a Zelfstudie Literature reading, preparation presentation n/a
2 Fri 11-Jan 9.30-10.00 IB L/ intro Protocol gelelectrophoresis & protein staining CCA 3.38
2 Fri 11-Jan 10.00-17.00 RdH, IB PR gel electrophoresis and protein staining CCA lab
WEEK 2 Rooster Optional Master “Biomedical Proteomics" ; M_CPROTBI09
Theme 2 Proteomics in Practice Coordinator: CR Jiménez
Global quantitative proteomics
Week/day/date duration Staff Form Subject Room
3 Mon 14-Jan 9.30-17.00 RdH, OPL PR In-gel digestion of proteins CCA lab
3 Tue 15-Jan 9.00-13.00 RdH, OPL PR Peptide extraction and sample preparation for mass spectrometry CCA lab
3 Tue 15-Jan 13.00-14.00 SP demo LC-MS of peptide samples CCA mass spec lab
3 Tue 15-Jan 14.00-15.00 SP L Data processing and data mining CCA 1.34
3 Tue 15-Jan 15.00-17.00 n/a Zelfstudie Literature reading, preparation presentation n/a
3 Wed 16-Jan 9.00-12.30 n/a Zelfstudie Literature preparation presentation n/a
3 Wed 16-Jan 13.30-17.00 DK, FR PR Literature study: presentation CCA 1.06
3 Thu 17-Jan 9.30-10.30 CRJ L Data mining using GO and pathway tools CCA 1.34
3 Thu 17-Jan 11.00-14.30 FR, OPL PR Data mining PK 1Y 145
3 Thu 17-Jan 14.30-15.00 CRJ Q&A vragenhalfuurtje PK 1Y 145
3 Thu 17-Jan 15.00-17.00 n/a Zelfstudie Literature reading, preparation exam n/a
3 Fri 18-Jan 9.00-14.00 n/a Zelfstudie Preparation exam n/a
3 Fri 18-Jan 14.30-16.30 CRJ EXAM CCA 3.38
L=lecture (hoorcollege); PR=  practical lab work
CRJ= Connie Jiménez
SP= Sander Piersma
RdH= Richard de Haas
DK= Diederik Kuster
FR= Frank Rolfs
IB= Irene Bijnsdorp
Proteomics= 3 credits cursus

Tutorial Figures

Protein identification by mass spectrometry-based proteomics

Biomarker discovery and validation pipeline

Process flow for the development of novel biomarker candidates. Each of the five biomarker development phases has its specific aims and requirements. Experiment size refers to the numbers of proteins expected to be evaluated as candidate biomarkers in each phase of development in relation to the sample requirements. Adapted from Suriniva et al., J.Proteome.Res. 10(1), 5-16 (7-1-2011).

OPL Meetings

Every Friday 14.00-~15.30/16.00.

All lab members present updates on their research. Collaborators are welcome to join in and present their work as well.

Journal club
Bi-weekly on Fridays 13.00-14.00 and sometimes on another day.

Medical Oncology Dept. seminar:
Every Friday 16.00-17.00.
CCA NeXt and CCA seminars
Ad hoc