Types of Analysis

In the last decade or two, advances in mass spectrometry allow it to be applied to quantitative and qualitative analysis of compounds that are volatile or involatile. Modern separation methods combine in powerful ways with mass spectrometry.

Proteomic analysis

Proteomic approaches have enabled the identification of thousands of differentially expressed proteins in complex mixtures and also ushered the capability of discriminating disease subtypes/aggresiveness that are not recognised by traditional criteria.  Thus, it offers a platform for the identification and quantification of proteins and may uncover new therapeutic targets.  Translation of protein biomarkers in FDA approved diagnostic can be carried out at BMSF.

Some examples of what we can do include:

  • Quantitative analysis (iTRAQ, comparative proteomics, MRM)
  • Protein modification determination
  • Separations (pre-fractionation, SDS-PAGE, 2D-gels)
  • Analysis of tryptic digests, gel-fractions and peptides in biological extracts
  • Determine pancreatic polypeptide levels in human plasma
  • Mass determinations of intact proteins/glysosylations level estimation
  • Top/Middle Down protein analysis by ECD, ETD, and IRMPD
  • Development of phosphorylation assays used to investigate cell-signalling
  • Phosphopeptide analysis by TiO2, IMAC and anti-phosphotyrosine enrichment
  • Low mass peptide/protein (<25kDa) enrichment from complex proteomes
  • nanoLC-MS/MS protein digest analysis (LysC, AspN, Chyotrypsin etc)
  • De novo sequencing of peptides and small proteins
  • Mascot, SEQUEST, MaxQuant or PEAKS searches for protein identification
  • iTRAQ analysis and quantitation
  • SILAC analysis and quantitation
  • High resolution UPLC label free protein quantification 
  • Static nanospray of peptides and proteins including antibodies
  • MALDI-ToF tissue imaging
  • Interpretation of results
  • SWATH (data independent acquisition)


Metabolomic Analysis

Alternations in cellular metabolism are hallmark features of metabolic dysfunction, cancer, infection, inflammation, and neurobehavioural disorders.  The BMSF Small Molecule team trains students and researchers on the use of MS-based methods to conduct targeted measurements of small metabolites (<1kDa) using stable isotopes and in global metabolite profiling.

These metabolites provide valuable understanding of major metabolic pathways and their quantification helps elucidate mechanisms underlying cell energy/homeostasis and disease pathology.  Biological samples include cultured cells, bodily fluids, and tissue extracts.

Some examples of what we can do include:

  • Acylcarnitines
  • Aminoacids
  • Organic acids
  • Isotope dilution GC/MS or LC/MS assays
  • Analysis of catecholamines
  • Kynurenine Pathway metabolite identification
  • Nitrates and Nitrites analysis
  • Glucose quantification
  • Hormone identification and quantification
  • Acetylcholine and other quaternary ammonium biological amines
  • Quantification of Vitamin D and metabolites
  • Assay for the quantification of dityrosine in urine and protein hydrolysates
  • Detection of lactones in microbial extracts
  • Analysis of coal tar samples for molecular weight distribution
  • Analysis of borate complex structure in plant extracts
  • Metabolite profiling by LC-MS or GC-MS
  • Untargeted metabolomics
  • Orbitrap LC-MS for accurate mass small molecule analysis
  • Triple quadrupole LC-MS for small molecule analysis
  • Ion trap LC-UV-MS for small molecule analysis
  • Small molecule quantitation by mass spectrometry
  • Drug quantitation in biological fluids by mass spectrometry
  • Targeted quantitation of specific molecules in biological fluids/tissues by mass spectrometry
  • Folate quantitation

Small Molecules

Our small molecule analysis work includes accurate mass analysis with mass-to-charge measurement accuracy of 2ppm using an LTQ-Orbitrap XL MS with static nanospray.  This is used to confirm synthetic target structures and to narrow the range of possible elemental formulae for unknowns.  Isotopic fine structure data for unknowns can also be determined.


Volatile organic compounds (VOC's) in the headspace above aqueous sample solutions can also be determined by both direct headspace sampling and by solid phase microextraction (SPME).  Typical applications include odor analysis, novel cancer screening technologies, quantifying methanogenesis in the headspace above cultured bacteria and analysis of permanent organic and inorganic gases.

Lipidomic analysis

Lipids have low water solubility and comprise a broad range of structurally diverse molecules, including fatty acids, waxes, eicosanoids, monoglycerides, diglycerides, triglycerides, phospholipids, sphingolipids, sterols and steroids, terpenes, prenols and fat-soluble vitamins.  Lipids are commercially important as food, in the production of biodiesel and other manufacturing processes, and they perform a wide variety of biological functions.

Key roles include energy storage, cell membrane structure and signalling molecules.  Considerable research demonstrates that changes in lipid species and lipid damage significantly influence the development of disease by a range of mechanistic pathways.

We have experience in:

  • Isotope dilution GC/MS or LC/MS quantification
  • Lipid analysis or profiling by high resolution LC-MS and MS/MS
  • Quantification of lipids by nanospray
  • Lipid extraction
  • "Non-targeted" qualitative and quantitative analysis of
    • Glycerolipids
    • Phospholipids
    • Sphingolipids
  • "Targeted" quadrupole MS analysis of
    • Sterols and steroids
    • Total fatty acid profiles

Isotope Ratio Mass Spectrometry (IRMS)

The BMSF has capabilities for the stable isotope analysis of carbon and oxygen isotopes for small inorganic carbonate samples, such as used in the analysis of stalagmites, coral, and bone apatite. Applications include environmental sciences, geosciences, forensic science, and archaeological sciences, measured using a MAT253 and Kiel IV carbonate device.

We also have compound specific and bulk organic isotope capabilities for carbon, nitrogen, oxygen, and hydrogen isotopes.

Our HTEA-GM-IRMS has a wide range of environmental and forensic applications, including tree cellulose records of environmental change, environmental lipids and food web studies, and the analysis of archaeological collagen.

We offer services with:

  • Kiel/IRMS analysis of carbonate
  • Elemental Analysis/IRMS

Desorption Electrospray Ionisation (DESI)

The DESI technology is a simple, sensitive, gentle, and versatile ionization method that allows for the direct sampling of surfaces without any sample preparation and under ambient temperature and pressure conditions. This patented technology (patent #7335897) was first disclosed in Science, Vol. 306, #5695, pp. 471-473, October 2004.

Other Techniques and Capabilities

  • Imaging Mass Spectrometry (IMS)
  • Analysis of synthetic polymers and large synthetic organometallics
  • HPLC separations
  • UPLC separations
  • nano-DSC
  • nano-iTC
  • Data analysis and bioinformatics software
  • Synthetic Biology.  Many of the analytical capabilities of the BMSF may be utilized in research area.