Services

Comprehensive proteomics support from sample to insight

We provide end-to-end proteomics services covering sample preparation, high-resolution LC–MS/MS measurement, and advanced quantitative data analysis. Our facility supports discovery proteomics, targeted questions, post-translational modification studies, and microdissected tissue workflows.

1. Sample preparation

We offer high-quality preparation of diverse biological materials, ensuring clean, reproducible peptide samples optimized for mass spectrometry.

Standard workflows

FASP (Filter-Aided Sample Preparation)
In-gel digestion
LCM-derived sample processing (laser-capture microdissected samples)
Tryptic digestion and peptide cleanup

Advanced enrichment and labeling

Phosphopeptide enrichment for phosphoproteomics (other enrichment strategies for post-translational modifications available after discussion)
TMT labeling for multiplexed quantitative studies (available on a per-project basis)

2. LC–MS/MS acquisition

We generate high-resolution proteomic data using state-of-the-art liquid chromatography–tandem mass spectrometry (Vanquish Neo UHPLC coupled with Orbitrap Ascend).

Capabilities

Standard 30-minute LC–MS/MS gradients
Flexible acquisition methods tailored to project needs
Suitable for:
- Discovery proteomics
- Quantitative studies
- PTM-focused investigations
- Small or challenging samples (e.g., LCM)
- Single-cell proteome analysis

3. Quantitative data analysis

Our computational pipelines provide robust, publication-grade insights.

What we deliver:

Quantitative DIA analysis (Spectronaut-based workflows)
Protein and peptide identification
Differential expression & statistical testing
Data visualization and figure-ready plots
Clear summaries suitable for interpretation and publication

4. Final deliverables

Every project includes complete, transparent data handover.

RAW LC–MS/MS files
Processed data reports (if analysis is included)
Methods summaries for manuscript use
Figure legends and ready-to-use graphics
Support in data interpretation and manuscript preparation (when appropriate)

Our approach

We maintain high scientific standards through:

Rigorous sample handling
Optimized and validated LC–MS/MS methods
Reproducible quantitative pipelines
Clear communication and shared interpretation of results

Frontier in proteomics: Single-Cell Proteomics (SCP)

A new frontier in proteomics is Single-Cell Proteomics (SCP).

SCP aims to unravel the diversity of protein expression within individual cells.
Access to SCP is possible through CellX - The Danish Single Cell Examination Platform.
Please contact us for more details.

MACSima

Sample preparation: tissue sectioning, deparaffinisation, antigen retrieval and antibody plate preparation.
Image acquisition: predefined panel programming, instrument setup, loading, acquisition checks and unloading.
Image processing and analysis: segmentation, cell phenotyping, spatial analysis and visualisation.
Custom development: panel design, antibody validation, methodological optimisation and advanced analysis, quoted according to project requirements.