Tampere University
Faculty of Medicine and Health Technology
Location: Kauppi-campus, Arvo Ylpön katu 34, Arvo-building, 3rd floor, room 315
33520 Tampere, Finland
Equipment Details and Descriptions
ZenoTOF 7600 (Sciex, 2024) – metabolomics and lipidomics
Liquid chromatography coupled with time-of-flight mass spectrometry (LC-TOFMS) is an analytical technique that separates compounds based on their chemical properties according to gradient flow. This process occurs in LC with a dedicated column that contains particles capable of retaining hydrophobic or hydrophilic compounds. From the LC column, the compounds are then ionized and identified based on their mass-to-charge ratio and fragmentation patterns.
Our instrument (ZenoTOF 7600, Sciex) has broad usage capabilities and offers analysis for small- and large-scale studies, including targeted and untargeted (discovery) analysis, qualitative analysis with the primary outcome detected or undetected, as well as quantitative analysis. We use the SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment Ion spectra) method with collision-induced dissociation (CID) or electron-activated dissociation (EAD). CID is more aggressive in breaking the molecule than EAD, which is gentle and critical in the structural elucidation of a molecule. Other methods, such as data-dependent acquisition (DDA), can be used depending on the research questions.
We look for chemicals such as pesticides, herbicides, polyfluoroalkyl substances (PFAS), antibiotics and other pharmaceuticals, organic contaminants, and protein assessment, or methods that can be tailored to the customer’s needs. We are expanding our specialisation to cover clinical samples and perform metabolomics and lipidomics, including the possibility of analysing bile acid lipids. Our facility is also specialized in environmental matrices such as wastewater and sludge for the purpose of using wastewater as surveillance for indication of public health. The facility can provide full service with sample preparation, analysis, and bioinformatics if needed.
For example, the untargeted study includes sample preparation, method run, quantitation or qualitative, library creation or search, results, and bioinformatics. For metabolomics and lipidomics studies, sample preparation is critical.
Below are possible samples that can be processed:
-Body fluid (tear, blood, plasma, urine)
-Tissue and cell lysate
-Cell culture medium
-Extracellular vesicles
-Pull-down mixture
-Protein band from SDS-PAGE gel
-Wastewater and sludge
We are still building the library for small molecules; please enquire if we already have one that suits your needs.
TripleTOF 5600+ (Sciex) – proteomics
Nano LC-MS/MS liquid chromatography-mass spectrometry (tandem Quadrupole Time-of-Flight mass spectrometer TripleTOF 5600+ coupled with an Eksigent 425 Nano LC system, AB Sciex, Concord, Canada) is an analytical technique, where compounds are first resolved chromatographically using a gradient flow, and then ionized and identified based on mass spectral data of the compounds of interest and their fragmentation patterns.
The facility has broad proteomics capabilities offering analysis for small and large-scale studies, including basic protein identification studies as well as clinical trials/discovery studies, and has specialised in label-free relative quantitation of proteins from small clinical samples using SWATH-MS method. A protein discovery study includes, sample preparation steps like enzymatic digestion of the proteins to peptides, data dependent acquisition (DDA) runs for the identification of the proteins and for the library creation required for quantification studies. SWATH-MS analysis is carried out for relative quantitation of proteins. Typical study using tissue samples or cell lysates with relatively simple sample handling yields 3000-4000 relatively quantified proteins per sample.
For samples submitted for identification studies, results will be provided indicating the proteins identified in the order of best score, and their sequence coverage. For samples related to quantification studies and bioinformatics kindly contact us for more information. We are happy to discuss your needs further!
ACKNOWLEDGEMENT
All the users of the Mass Spectrometry Facility services are obligated to acknowledge the facility in publications:
“The authors acknowledge the Tampere Mass Spectrometry Facility for their service.”