Equipment and capabilities
Equipment
LC mass spectrometers
Agilent 6520 accurate mass (2-5 ppm) quadrupole time of flight (QToF) mass spectrometer
Agilent 6410 triple quadrupole (QQQ) mass spectrometer
- Each interfaced to liquid chromatography (LC) via ESI or APCI sources.
- The LC systems comprise Agilent 1200 SL binary pumps capable of rapid high-resolution chromatography to separate analytes before delivery to the MS.
- Various LC column types to separate molecules of varying chemistry.
GC-QToF mass spectrometer
GC-QToF MS/MS with EI and CI sources
- Accurate mass (2-5 ppm) measurement of volatile compounds
- Many non-volatile compounds can be derivatised prior to analysis to make them volatile.
HPLC system
High-performance liquid chromatography (HPLC) system
- Quaternary LC pump
- Photodiode array
- Refractive index
- Fluorescence detectors
- Fraction collector to collect compounds of interest.
Capabilities
Examples of types of research supported are:
Measurement of specific sets of compounds in tissue/cell extracts
Including:
- Sugars
- Amino acids
- Glycolysis/TCA cycle intermediates
- Flavonoids
- Hormones
- Isoprenoids
- Antioxidants
- Specialised/secondary compounds
- Fatty acids
- Lipids
- Drugs
- Organic pollutants
and many others.
Untargeted metabolite profiling (metabolomics)
- To identify differences in chemical composition and relatedness between samples (for example caused by mutations or experimental treatments).
Identification of unknown compounds using accurate mass, isotope abundance and MS/MS fragmentation
- For example: compounds of interest from untargeted profiling and products from enzyme reactions or synthetic chemistry.
- This identification often also requires confirmation by other analytical techniques such as NMR and IR spectroscopy, which complement our mass spectrometry capabilities.
Measurement of metabolic flux or identification of metabolic pathways
- Using stable isotope labelled (e.g. 13C and 15N) precursors.
- Labelling of specific atoms in labelled products is detected by their increased mass.
Data storage
- Data files and metadata are stored on a dedicated server to comply with funder requirements and enable re-use.
Cross-facility capabilities
Mass Spectrometry can work in conjunction with:
- Bioimaging
- Cytomics
- Sequencing
To help provide more comprehensive answers to complex research questions.
Data analysis facilities
MassHunter Qualitative Analysis
Data inspection and general analysis:
- Deconvolve raw data to extract potential compounds
- Extract MS and MS/MS data for compounds
- Predict molecular formula
- Database searches
- Export reports.
MassHunter Quantitative Analysis
- Extract peak areas from samples/standards for quantitative analysis of known and unknown compounds.
- Export spreadsheets.
MassHunter Profinder
- Automated extraction of compounds and correction for retention time drift across multiple raw data files from metabolite profiling experiments.
- Export to spreadsheet or Mass Profiler Professional (MPP) to compare compound abundance across samples.
Mass Profiler Professional (MPP)
- Import compound information from Mass Hunter Profinder for statistical analysis (ANOVA, clustering, PCA etc).
- Database (IDBrowser + PCDL) searching for preliminary compound ID (detailed ID for specific compounds in MassHunter Qualitative Analysis).
- Integration of metabolomic and transcriptomic datasets.
- Accessed via MS facility data analysis computer.
Personal Compound Database and Library Manager (PCDL) for LC-MS
- Bespoke compound lists (plus MS/MS spectra imported from MassHunter Quantitative analysis).
- Searchable from MassHunter Quantitative analysis and MPP for compound identification.
Mass Spectral Librarian for GC-MS
- Very large library of MS/MS spectra searchable via MassHunter Qualitative Analysis.
- Includes the NIST mass spectral library.
- Bespoke libraries can be prepared from our GC-MS data.
Open-source software
- The metabolomics community has developed many online and downloadable data analysis pipelines.
- The MS Facility can advise on the use of a number of these.
