Mass Spectrometry Facility

Capability A of the La Trobe Comprehensive Proteomics Platform (LTU-CPP)

This state of the art facility, situated within the La Trobe Institute for Molecular Science (LIMS) offers a comprehensive range of different types of mass spectrometry equipment. Services include qualitative and quantitative mass spectrometry; HPLC sample fractionation, Advion TriVersa Nanomate robot front end, 2D SDS-PAGE and OFFgel electrophoresis. The facility is a member of the Victorian Platform Technologies Network.

Equipment (Mass spectrometers)

QExactive HF Hybrid Quadrupole Orbitrap Mass Spectrometer (Thermo Scientific)

This system (installed end 2015) combines a state-of-the-art segmented quadrupole for high-performance precursor ion selection with a high-resolution, accurate-mass (HR/AM) ultra-high-field Orbitrap mass analyzer to deliver a superior combination of scan speed, resolving power, mass accuracy, spectral quality and sensitivity. The Q Exactive HF is used for quantitative work on samples with high complexity. The system is coupled to a nanoUPLC Ultimate 3000 system (Thermo-Scientific) with flow rate of 250 to 600 nL/min.

LTQ Orbitrap Elite ETD (Thermo Scientific)

The Orbitrap Elite is a high performance hybrid mass spectrometer combining the high-field Orbitrap mass analyzer with the latest dual pressure linear ion trap, allowing increased speed, sensitivity and dynamic range. It can achieve mass resolutions of 240,000 with mass accuracy typically < 3 ppm with external calibration making it ideal for analyzing high complexity proteomics samples.

The LTQ Orbitrap Elite supports a variety of different fragmentation techniques. In the characterization of post-translational modifications, especially labile modifications such as phosphorylation and glycosylation, ETD is a very valuable tool that complement the typical Collision Induced Dissociation (CID). The Elite is also equipped with High energy C-trap Dissociation (HCD) which provide peptide fragmentation technique used in iTRAQ and TMT quantification approaches.

It is equipped with the heated ESI (H-ESI II) and the nanoESI (nanoSpray Flex Ion) sources, as well as the nanochiped based infusion Advion TriVersa Nanomate®.

The Elite is coupled to a nanoUPLC Ultimate 3000 system (Thermo-Scientific) with flow rate of 250 to 600 nL/min.

TSQ Vantage Extended Mass Range (Thermo Scientific)

The TSQ Vantage is a triple quadrupole mass spectrometer. This instrument is capable of scan functions, such as Selective Ion Monitoring (SIM), Selective/Multiple Reaction Monitoring (S/MRM), and precursor ion scanning. This is the instrument of choice for qualitative and quantitative analysis of targeted peptides from complex mixtures and for quantifying small molecules.

The extended mass range option offers higher resolution, higher resolution precursor selection, and an extended mass range of up to 3000 Daltons. This instrument is coupled to a nanoUPLC Ultimate 3000 system (Thermo-Scientific) for performing LC-MS at flow rates ranging from 250 to 600 nL/min.

LC-Isolink Isotope ratio mass spectrometer (Thermo Scientific)

The LC-IRMS facility consists of an Accela autosampler and Accela 600 pump attached to a Delta V plus isotope ratio mass spectrometer via an LC-Isolink.

It is capable of analyzing stable isotope ratios of carbon (δ13C) at natural abundance in aqueous samples. It is mainly used for non-volatile compounds such as amino acids, carbohydrates and amino-sugars that can be analysed without the need of derivatisation to make them more volatile (as required for GC-IRMS analysis). Samples can be measured in bulk (approx. 500ng of C) or using liquid chromatography (approx. 10μg of protein on column) to separate out components of complex mixtures for compound specific isotope analysis (CSIA).

MALDI TOF/TOF (Bruker Daltonics) Ultraflex III MALDI-TOF/TOF MS with 'Smartbeam' Laser

The Ultraflex III is a Matrix Assisted Laser Desorption / Ionization time-of-flight mass spectrometer (MALDI-TOF/TOF) that provides the high resolution and mass accuracy required for analysis of a wide range of biomolecules. Features include:

  • Fragmentation analysis or sequencing of peptides
  • Mass accuracy to within 150-300 ppm for proteins
  • MS/MS for de novo sequencing of peptides
  • LC-MALDI proteomics workflow
  • Proteineer fc MALDI-spotting robot (see below)
  • 384 MTP format
  • Transponder coding for sample tracking.

MicrOTOF-Q (Bruker Daltonics)

The micrOTOF-Q, a benchtop ESI-Q-q-TOF mass spectrometer, is equipped for requirements in metabolomics, proteomics and drug development. Features include:

  • Suitable for de novo sequencing of peptides
  • Online NanoElectrospray source
  • Dionex Nano LC
  • Mass accuracy 3 ppm with internal calibration
  • Mass accuracy 5 ppm with external calibration.

HCTultra (Bruker Daltonics) PTM Discovery System Ion-Trap MS with Electron Transfer Dissociation sources

Electron transfer dissociation (ETD) is a fragmentation technique that preserves post-translational modifications. ETD MS/MS spectra of peptides can be collected on-the-fly during LC/MS/MS runs using the HCTultra PTM Ion Trap. Features include:

  • Online NanoElectrospray source
  • Dionex Nano LC.

Esquire 6000 (Bruker Daltonics)

The Esquire 6000 uses an electrospray ion source (ESI) for mass identification and sequencing of small molecules, peptides and macromolecules.

Licensed Software

  • Mascot v2.4
  • MaxQuant
  • SequestHT
  • Proteome discoverer 2.0
  • Scaffold batch Q+S


For more information about accessing the LIMS Mass Spectrometry Facility, please contact:
Dr Pierre Faou
T: +61 3 9479 2402