Institute for Future
Environments

Proteomics and small molecule mass spectrometry

Overview

Our proteomics and small molecule mass spectrometry laboratory is part of the Central Analytical Research Facility (CARF).

We are equipped with a number of state-of-the-art mass spectrometry platforms that allow for a range of tests, including qualitative, quantitative and structural analysis of proteins, lipids, metabolites, pesticides, pharmaceuticals and volatile organic compounds. Tests can be performed as long as the molecules of interest are amenable to ionisation technique employed in the source of a mass spectrometer. Depending on the instrument type, samples may be solid, liquid or gas.

The mass spectrometry platforms in our laboratory can be broadly divided into two main categories:

  • Liquid Chromatography Mass Spectrometry (LC-MS)
  • Gas Chromatography Mass Spectrometry (GC-MS).

Research applications

Modern mass spectrometry instruments can be used across a broad range of fields and applications including:

  • volatile organic compounds (odour analysis)
  • pharmacokinetics (bioavailability, bioefficacy)
  • drug development (determining structures of drugs and metabolites)
  • clinical testing (biomarkers discovery and endogenous compounds)
  • genomics (oligonucleotide sequencing)
  • epigenetics (global DNA methylation analysis)
  • environmental research (testing water, soil, food and air quality).

Typical projects

Projects we've been working on include:

  • next generation clinical veterinary proteomics using SWATH (Sequential Window Acquisition of all THeoretical Mass Spectra) approach
  • protein biomarkers of wound healing
  • cancer lipidomics and proteomics
  • metabolomics approach to study effect of diet on fruit fly sexual selection
  • fruit volatiles and synthetic lure formulation
  • global DNA methylation analysis into pest resistance to bio insecticides
  • volatile compounds in animal reproduction and animal breath
  • analysis of extractables and leachables on medical devices.

Read details

Laboratory Coordinator

Laboratory team

Organisational unit
Lead unit Institute for Future Environments Other units
Research areas
Keywords
mass spectrometry, quantitative proteomics, metabolomics, lipidomics, liquid, chromatography, gas chromatography, LCMS, GCMS, thermal desorption, volatile organic compounds, VOC, Sequential Window Acquisition of all Theoretical Mass Spectra, SWATH-based quantitative proteomics, proteomics
 

Details

Liquid chromatography mass spectrometry (LC-MS)

Instrument Capabilities and features
SCIEX TripleTOF 5600+ LC-MS/MS platformCoupled to Eksigent nano flow HPLC, this hybrid quadrupole Time-of-Flight (QqTOF) mass spectrometer is a high sensitivity, high resolution and high mass accuracy discovery and quantitation platform with variable windows SWATH acquisition capability. Application to label free-quantitative proteomics.
SCIEX TripleTOF 6600+ LC-MS/MS platform Coupled to Eksigent nano flow HPLC, this hybrid quadrupole Time-of-Flight (QqTOF) mass spectrometer is the most sensitive SWATH-enabled platform available on the market. Application to label free-quantitative proteomics.
Shimadzu Triple Quadrupole 8050 LC-MS/MS platform Coupled to Nexera ultra high performance liquid chromatograph (UPLC) this triple quadrupole (QqQ) mass spectrometer is a high sensitivity and ultra-fast polarity switching verification platform with ESI and APCI ionization capabilities. Application to targeted quantitation (MRM-MS) of trace-level semi-volatile/non-volatile compounds such as nucleotides, pharmaceuticals, metabolites and lipids.
SCIEX Triple Quadrupole Trap 6500 LC-MS/MS platform Coupled to Prominence high performance liquid chromatograph (HPLC) this triple quadrupole (QqQ) mass spectrometer is a high sensitivity verification platform with differential ion mobility (DMS) and ozonolysis (OzID) capabilities for enhanced separation/structural elucidation of isobaric compounds and epimers. Application to shotgun lipidomics.

Gas chromatography mass spectrometry (GC-MS)

Instrument Capabilities and features
Thermo Scientific Single Quadrupole ISQ Series TD-GC-MS platform Equipped with gas chromatograph and Markes TD-100 thermal desorption unit. Application to full MS and SIM-MS scans-based analysis of volatile organic compounds.
Thermo Scientific Triple Quadrupole TSQ 8000 Evo HS/SPME-GC-MS/MS platform Equipped with gas chromatograph and TriPlus RSH autosampler with liquid injection, SPME and headspace (HS) sample introduction capabilities. Application to full MS and MRM-MS scans-based quantitation of trace-level volatile/semi-volatile compounds in complex samples.
Shimadzu Triple Quadrupole 8040 GC-MS/MS platform Equipped with gas chromatograph and Gerstel autosampler with liquid injection, SPME and headspace (HS) sample introduction capabilities. Application to metabolite profiling with online TMS derivatisation.
Thermo Scientific Q Exactive GC Orbitrap GC-MS/MS platform Equipped with gas chromatograph and TriPlus RSH autosampler with liquid injection, SPME and headspace (HS) sample introduction capabilities this hybrid quadrupole Orbitrap mass spectrometer is a high sensitivity and high mass accuracy discovery and quantitation platform delivering high resolution GCMS data.

Sample preparation

Instrument Capabilities and features
Benchtop preparation Bench area for sample and reagent preparation. Includes ultra-high purity solvents and chemicals, proteolytic enzymes, derivatisation reagents, keratin-free environment, shakers, incubators, temperature-controlled centrifuges and the below listed equipment.
Martin Christ Rotational vacuum concentrator Drying or concentrating samples with or without heating.
Eppendorf Thermomixer Programmable heating, cooling and mixing. Adapters for various tube and plate formats available.
Bio-Rad and Invitrogen SDS-PAGE equipment Selection of polyacrylamide gel electrophoresis (PAGE) equipment for fractionation of proteins. Compatible with self-cast and pre-cast gels from various suppliers.
Perkin Elmer JANUS G3 MDT Automated WorkstationLiquid handling system for automated sample preparation.
Agilent 3100 OFFGEL fractionator Gel-free fractionation of peptides and proteins using isoelectric focusing (IEF).

Bioinformatics pipelines and tools

InstrumentCapabilities and features
Commercial SWATH-based quantitative proteomics pipelineIncludes Mascot, ProteomeDiscoverer, ProteinPilot, PeakView, and MarkerView.
Open source SWATH-based quantitative proteomics pipelineIncludes X!Tandem, Seaquest, DIAUmpire, SwathXtend, Skyline, and MSstats.

Services and equipment hire

Accessing services and equipment

Our equipment and services are available to QUT staff and students, external researchers and commercial clients with both self-service (unassisted) and full-service (with technical assistance) options as listed below.

Due to the complex nature of most mass spectrometry experiments, we would appreciate if all potential clients could complete the Project Scope Form (PDF file, 508.8 KB) to allow us to assess the feasibility of the analysis, timeframes and costs. Please email the completed form and we will contact you shortly.

With technical assistance/service

Service description External researchers
(1 month turnaround)
Commercial organisations
(10 working days turnaround)
Proteomics (per hour) $130 $315
LC-MS (per hour)$130 $315
GC-MS (per hour) $95 $220
Technical staff assistance with sample preparation, data analysis, report preparation (per hour)$115$115
Targeted method development/transfer (per compound and co-authorship) $3,150$6,300
Pilot/trial run (per sample)$525$525

Conditions

  • Additional method development fee will apply to new samples that we are dealing with for the first time or non-conventional samples requiring non-routine analysis.

Annual subscription fee for unassisted use

Service description External researchers Commercial organisations
LC-MS access and training (per year) $6,300 $18,000
GC-MS access and training (per year) $2,100 $6,000
Proteomics (per year)$6,300$18,000

Conditions

  • The access and training fee covers 300 hours of instrument or technician time and is to be used within 12 months.
  • The fee covers access to the laboratory for a single user, basic training on specific instrumentation, and basic training in limited number of software tools.
  • The fee does not cover assistance in sample preparation, method development and data interpretation. A separate arrangement must be made for this service.
  • Full fee must be paid up front and unused hours will not be transferred to another user, or beyond specified period, or reimbursed in any way.

Quantitative proteomics package (per batch)

This service package is for label-free quantitative profiling of proteins in 6 to 12 samples using data-independent acquisition (SWATH-MS). It includes sample preparation, data acquisition, data processing and statistical analysis. The client will be provided with the list of proteins that showed statistically significant fold change, proteins that showed no change, a volcano plot of a publishable quality, and the minimum information on the method used for publication purposes. Raw (unprocessed) data can also be provided on request.

Image of an example sample volcano plot and a corresponding results sheet
Image of an example sample volcano plot and a corresponding results sheet.

Service description External researchers
(4 months turnaround)
Commercial organisations
(2 months turnaround)
Sample prep and data acquisition $6,000 $18,000
Bioinformatics $3,000 $9,000

Conditions

  • Any additional set of 6 to 12 samples submitted as part of the original batch will incur a fee of $3,000.
  • An additional method development fee will apply to non-conventional requests, (ie. post-translational modification, subcellular fractionation, time point study).
  • The number of proteins quantified will depend on the type of sample and availability of genomic information, (ie. undepleted human plasma ~ 250 proteins, human cell line ~ 2,500 proteins).
  • Only a single protein isoform will be reported per group of homologous proteins.
  • A minimum 20 ug protein per sample is required.
  • A spectral library generated as part of the project, will remain property of CARF.

Contacts

Central Analytical Research Facility - Proteomics and Small Molecule Mass Spectrometry Laboratory


  • Gardens Point
    2 George St
    Brisbane QLD 4000
    Australia