Mass spectrometry

The NORBRAIN mass spectrometry unit delivers high sensitivity for the quantitative analysis of small molecules, peptides, toxins and drugs. We provide expertise, services, education, and training to enhance biomedical research through mass spectrometry-based technologies. Currently, two scientists and one technician run the facility.

Equipment and software

We use the Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer and the Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer.

Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer

High resolution and accurate mass (HR/AM) analysis on the NORBRAIN Q‐Exactive mass spectrometer presents a unique configuration: the combination of the orbitrap mass analyzer with a quadrupole mass filter for precursor ion mass selection enables new quantitative methods based on HR/AM measurements, including targeted analysis in MS mode (single ion monitoring, SIM) and in MS/MS mode (parallel reaction monitoring, PRM).

The ability of the quadrupole to select a restricted m/z range allows overcoming the dynamic range limitations associated with trapping devices like the Orbitrap XL. Therefore high end quantitative and qualitative analysis in the area of in drug discovery, proteomics, environmental and food safety, clinical research and forensic toxicology can be offered. For example a proteomic discovery analysis on the Q-Exactive allows the detection of several thousand proteins in one run (180 min gradient).

Thermo Scientific TSQ Vantage Triple Stage Quadrupole Mass Spectrometer

Delivers high sensitivity for the quantitative analysis of small molecules, peptides, toxins and drugs. It is coupled online to a Dionex LC-system (Thermo-Fisher Scientific) and offers selected-reaction monitoring of peptide for protein quantification with an extended mass range of up to 4000 m/z.

Both complementary mass spectrometry systems (TSQ Vantage and Q-Exactive) therefore allow to develop high throughput biomarker analyses (TSQ Vantage) based on the suggested biomarker candidates from previous Q-Exactive MS analyses.

Software

  • Database search tools: Sequest (Proteome Discoverer 1.4)  for tandem mass spectra interpretation
  • MaxQuant/ SIEVE for relative quantification
  • In-house software tools (SAPA- and peptide mass tool) for protein peptide analyses

Services

Our primary focus is on epiproteomics, protein and lipid profile characterization as well as metabolomics and small molecule analysis. One of the main focuses is the analysis of post-translational modifications. Protein identification is performed on a regular basis.

Protein analyses offered include in-gel or in-solution protease digestion, chromatographic separation and tandem mass spectrometric analysis of the generated peptides, and interpretation of MS/MS data using software like Sequest, Mascot, and MaxQuant.

The facility also assists especially in applications for the isolation (enrichment strategies like lectin chromatography), detection and characterization of post-translationally modified peptides (e.g. phosphorylation, N- and O-linked glycosylation, oxidation, ubiquitination, cysteine modifications, acetylation/ methylation (+ di- and tri-methylation) and O-GlcNAc modification). Sites of modification are verified by manual inspection of the data.

Please consult facility staff for projects which implements specialized approaches related to proteomic PTM analysis. Also we offer service related to quantitative protein expression profiling (SILAC, N15 labeling, LFQ=label free quantification).

If you have any questions about consultations regarding experimental design and proteomic analysis options please contact us by e-mail: norbrain-ms@medisin.uio.no


Photo: Gunnar F. Lothe, Institutt for medisinske basalfag, UiO.