Resources

Resources

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.

Infrastructure

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

Software

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.


Education

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.

More information for master students.

PROTEOMICS IN BIOMEDICAL RESEARCH-2018

see also from VU University website

Click here for an impression of the 2018 course https://quik.gopro.com/v/nCPCXMVUV4/

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