Mass Spectrometry Facility

IMB’s Mass Spectrometry Facility is home to a suite of state-of-the-art mass spectrometry, high-performance liquid chromatography, and robotic instrumentation, that has been refined and optimised to investigate biological systems in a high-throughput qualitative and quantitative manner.

The facility enables researchers at IMB to investigate a broad range of mass spectrometric applications, including molecular discovery, identification, characterisation and quantification. They are gaining insights into protein interactions and structures, amino acid sequence, post-translational modifications, compound stability, and bioavailability of potential therapeutics in a range of biological systems.

Some of the recent discoveries made using the facility include the identification and characterisation of potential therapeutic molecules from natural product extracts using de-novo peptide sequencing, and revealing the quantitative bioavailability characteristics of new molecules in the discovery and development of potential therapeutic molecules for a number of diseases including chronic pain, breast and ovarian cancer, and chronic kidney disease.

Equipment available

Mass Spectrometry Instrument Descriptions and Capabilities

  1. 6600 Triple TOF Electrospray Quadrupole-quadrupole-Time of Flight
    • The most versatile and valuable instrument, current state-of-the-art
    • Very high mass accuracy and resolution (<1-5ppm, 30000-45000)
    • High resolution MS and MS/MS
    • Very fast scanning up to 100 scans per second
    • Duo TurboV, static nanospray and Ionspray sources
    • Nanospray source for high-sensitivity low-sample useage
    • DuoV source for high flow, high throughput applications
    • Most accurate for small molecule, protein and peptide determination
    • Accurate mass determination of organic molecules, 200-1200 Da
    • Low energy structure elucidation, MS/MS
    • MS/MS database searching for protein identification
    • High Resolution SRM Quantification
    • Good instrument for determination of posttranslational modifications, phosphorylation, glycosylation etc.
    • Lipidomics using positive and negative ion experiments
    • Proteomics and metabolomics
    • MS/MS All and SWATH (Variable mass window selection) experiments
    • High-throughput up to 30 analyses per hour with over 1200 protein identifications per hour using MS/MS database searching for protein identification
    • Protein expression quantification (ICAT/iTRAQ, no-label technology)
    • Combine with uHPLC, venom, peptide mapping, mass fingerprinting etc
    • Chemists, Biologists
       
  2. 5600 Triple TOF Electrospray Quadrupole-quadrupole-Time of Flight
    • Very high mass accuracy and resolution (<5ppm, 25000-40000)
    • High resolution MS and MS/MS
    • Very fast scanning up to 100 scans per second
    • Duo TurboV, static nanospray and Ionspray sources
    • Nanospray source for high-sensitivity low-sample useage
    • DuoV source for high flow, high throughput applications
    • Accurate mass for small molecule, protein and peptide determination
    • Accurate mass determination (<5ppm) of organic molecules, 200-1000 Da
    • Low energy structure elucidation, MS/MS
    • MS/MS database searching for protein identification
    • HRSRM Quantification
    • Determination of posttranslational modifications, phosphorylation, glycosylation
    • DNA/RNA using negative ion determination
    • Lipidomics using positive and negative ion experiments
    • Proteomics and metabolomics
    • MS/MS All and SWATH experiments
    • High-throughput up to 20 analyses per hour with over 1000 protein identifications per hour using MS/MS database searching for protein identification
    • Protein expression quantification (ICAT/iTRAQ, no-label technology)
    • Combine with HPLC, venom, peptide mapping, mass fingerprinting etc
    • Chemists, Biologists
       
  3. Agilent 6540 TOF Electrospray Quadrupole-quadrupole-Time of Flight
    • Very high mass accuracy and resolution (<5ppm, 20000-30000)
    • High resolution MS and MS/MS
    • Very fast scanning up to 20 scans per second
    • High Flow uHPLC source
    • Accurate mass for small molecule and peptide determination
    • Accurate mass determination of organic molecules, 200-1000 Da
    • Low energy structure elucidation, MS/MS
    • Chemists, Biologists
       
  4. ABI 5800 MALDI TOF-TOF MS MS/MS Time of Flight-Time of Flight (Tof-Tof)
    • Extremely high throughput for MS and MS/MS data acquisition using database searching on uninterpreted MS/MS data
    • High energy ms/ms for structural characterisation, CID MS/MS.
    •  Also provides more information for database searching algorithms especially at the low m/z range, i.e. immonium ions.
    • High mass accuracy and resolution, <5ppm and 40,000
    • The instrument of choice for extremely high-throughput proteomics.
       
  5. ABI 4000 QTRAP ESI-Quad-Linear Ion Trap
    • Most sensitive triple quadrupole mass spectrometer available
    • Nanoflow and static nanospray ion sources
    • Best instrument for quantification
    • Low/medium resolution structural identification
    • De-novo peptide sequencing
    • MS/MS and MS/MS/MS Product, Precursor, Neutral loss, MRM (Quantification)
    • Good for determination of posttranslational modifications, phosphorylation, glycosylation
    • Combine with HPLC, venom, peptide mapping etc
    • Chemists, Biologists
       
  6. QSTAR Elite Electrospray Quadrupole-quadrupole-Time of Flight
    • High mass accuracy and resolution (<5ppm, 8000-12000)
    • TurboIonspray, static nanospray and Ionspray sources
    • Nanospray source for high-sensitivity low-sample useage
    • TurboIonspray sourc for HPLC analyses
    • Good for HPLC analysis of proteins and peptides
    • Accurate mass determination of organic molecules, 200-1200 Da
    • Low energy structure elucidation, MS/MS
    • MS/MS database searching for protein identification
    • Good instrument for determination of posttranslational modifications, phosphorylation, glycosylation etc.
    • DNA/RNA using negative ion determination
    • Low-throughput 5-10 protein identifications per hour using MS/MS database searching for protein identification
    • Protein expression quantification (ICAT/iTRAQ, no label technology)
    • Combine with HPLC, venom, peptide mapping, mass fingerprinting etc
    • Chemists, Biologists
       
  7. QSTAR XL Electrospray Quadrupole-quadrupole-Time of Flight
    • High mass accuracy and resolution (5-10ppm, 8000)
    • TurboIonspray, static nanospray and Ionspray sources
    • Nanospray source for high-sensitivity low-sample useage
    • TurboIonspray sourc for HPLC analyses
    • Good for HPLC analysis of proteins and peptides
    • Accurate mass determination of organic molecules, 200-1200 Da
    • Low energy structure elucidation, MS/MS
    • MS/MS database searching for protein identification
    • Good instrument for determination of posttranslational modifications, phosphorylation, glycosylation etc.
    • DNA/RNA using negative ion determination
    • Low-throughput 5-10 protein identifications per hour using MS/MS database searching for protein identification
    • Protein expression quantification (ICAT/iTRAQ, no label technology)
    • Combine with HPLC, venom, peptide mapping, mass fingerprinting etc
    • Chemists, Biologists
       
  8. QSTAR Pulsar Electrospray Quadrupole-quadrupole-Time of Flight
    • High mass accuracy and resolution (5-10ppm, 8000)
    • TurboIonspray, static nanospray and Ionspray sources
    • Nanospray source for high-sensitivity low-sample useage
    • TurboIonspray sourc for HPLC analyses
    • Good for HPLC analysis of proteins and peptides
    • Accurate mass determination of organic molecules, 200-1200 Da
    • Low energy structure elucidation, MS/MS
    • MS/MS database searching for protein identification
    • Good instrument for determination of posttranslational modifications, phosphorylation, glycosylation etc.
    • DNA/RNA using negative ion determination
    • Low-throughput 5-10 protein identifications per hour using MS/MS database searching for protein identification
    • Protein expression quantification (ICAT/iTRAQ, no label technology)
    • Combine with HPLC, venom, peptide mapping, mass fingerprinting etc
    • Chemists, Biologists
       
  9. API 2000 Triple quadrupole mass spectrometer
    • Good instrument for quantification
    • Low-resolution structural identification
    • HPLC/MS complex mixtures
    • Bioavailability, pharmacokinetics
    • MS/MS Product, Precursor, Neutral loss, MRM (Quantification)
    • Combine with HPLC, compound purity
    • Chemists, Biologists
       
  10. Micromass LCT Electrospray Quadrupole-Time of Flight
    • Mass determination, good resolution (approx 2000-5000)
    • Workhorse for QA/QC of peptide plus organic molecule synthesis
    • Open-access instrument
    • Combine with HPLC, venom, peptide mapping etc
    • Chemists, Biologists
       
  11. Ciphergen SELDI-Time of Flight
    • Advantage over the other mass spectrometers with its technology of protein binding to affinity surfaces, antibody capture, ligand fishing, investigating biological matrices
    • Low throughput
    • Low resolution plus mass accuracy
    • Very expensive consumables (>$200 per chip approx $20 per sample alone) Biologists, clinical laboratory
       
  12. ABI 4700 MALDI Time of Flight-Time of Flight (Tof-Tof)
    • Extremely high throughput for MS and MS/MS data acquisition using database searching on uninterpreted MS/MS data
    • High energy ms/ms for structural characterisation, enables differentiation between leucine and iso-leucine for example. Also provides more information for database searching algorithms especially at the low m/z range, i.e. immonium ions.
    • Good mass accuracy, equivalent to the MALDI-Tof instrument
    • The instrument of choice for the extremely high-throughput proteomics laboratory
       
  13. HPLC/MALDI Robotics
    • Automated HPLC sample separation, MALDI preparation, analysis and database searching
    • High sensitivity nano, capillary and uHPLC systems
    • Shimadzu, Probot and Agilent robots for HPLC MALDI applications
       
    • Bioinformatics/Database searching
      • Protein Pilot 5.0, 4.5
      • Mascot

External users

Available systems include a suite of innovative mass spectrometers, such as a SCIEX MALDI ToF-ToF, an Agilent ES-ToF for high resolution small molecules, and a SCIEX 6600 triple ToF, arguably making IMB’s MS Facility the best in the country.

The facility currently assists over 150 different users from various institutions and fields. They have come to rely on IMB’s expertise and knowledge in both molecular science of natural products, and of the hardware and software of the various instruments at their disposal.

Our facility provides technical advice, research and training support, and can assist in the various stages of research, from concept through to experimental approach, including design, methodology, data acquisition and data processing, and project reporting and publication. Facility Manager Alun Jones has more than three decades of experience in biological mass spectrometry in both academia and industry in the UK, Canada and USA. During this time he has developed HPLC-mass spectrometry interfaces, methods of analysis for natural products, drug and pesticide analysis, peptide and protein analysis.

 

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