Getting access

Any project should begin with consulting lab manager Lene Holberg Blicher. Alternatively, a Project Creation Request can be submitted via our sample administration system, Stratocore PPMS. Instrument access will be allocated based on principles of project/instrument affinity and sample type. 

Before a project is initiated it is important to consider the following:

  • Sample complexity? Single proteins and low complexity samples are preferably analyzed on the Q-Exactive mass spectrometer, whereas high complexity samples are typically analyzed by on the H-FX or Fusion instruments.
  • Do you need to quantify the proteins between different samples? Are there replicates enough to ensure statistically valid quantification and does the dataset include appropriate control experiments? Do you need any labeling techniques or is label-free sufficient?
  • Post-translational modifications? Analysis of PTMs often requires dedicated sample preparation procedures and adapted mass spectrometry workflows. We readily support the analysis of phosphorylation events, and can help establish experimental workflows for other PTMs
  • How will the data be analyzed? Depending on the project, data may be more or less complex and time-consuming to handle. The core provides access to different data analysis software packages and can provide initial help to setup a workflow.

We kindly ask you to acknowledge the use of the proteomic core facility in publications in the appropriate acknowledgement section (e.g. Mass spectrometry analysis was performed at the DTU Proteomics Core, Technical University of Denmark.)

Sample preparation and QC

MS instrumentation is highly sensitive and it is therefore very important to carefully consider the experimental design to avoid contamination with for example polymers and detergents that are detrimental for instrument performance may compromise the analysis. All sample preparation must therefore be performed according to SOPs and using only mass-spec grade reagents and consumables. Experienced users can prepare samples themselves but the core lab technicians will always perform the last step in sample preparation.
Prior to handing in samples, please register an account and create a project on our sample administration system Stratocore PPMS. This system can be found here.
Samples are handed in either on washed StageTips, in original Eppendorf Brand micro tubes or in an otherwise specifically agreed format. Samples should be clearly labeled in an alpha-numerical way, for easy identification by facility employees. A sample manifest must be uploaded to Stratocore PPMS for sample identification.

Core Manager

Marie Vestergaard Lukassen

Marie Vestergaard Lukassen Proteomics Core Facility Manager