The Technique

Mass spectrometry (MS) has emerged as one of the most valuable tools in modern biology. In proteomics, MS facilitates the measurement of protein mass, protein identity as well as quantification with extraordinary sensitivity, speed and accuracy. MS can also be used to analyse other molecules such as lipids, glycans and oligonucleotides for identification and often quantification. Mass spectrometry is the core technology for ‘Omic’ research.

Facilities Available

  • ABSciex TripleTof 5600
  • ABSciex QTRAP 5500
  • Voyager DE STR MALDI-TOF
  • Shimadzu Prominence nano-LC system
  • Agilent 1100/1200 capLC system
  • Shimadzu Prominence UHPLC system
  • Various MS software programs (ProteinPilot, MRMPilot, MultiQuant, LipidView)


  The TripleTof 5600 mass spectrometer is a quadrupole-hybrid time-of-flight instrument. It is a sensitive state-of-the-art instrument with high resolution, mass accuracy and fast acquisition rates (~50 MS/MS per second), most suitable for discovery projects (ie what proteins are in my sample?), intact mass analysis (<10 ppm error) and quantification of labelled samples (ITRAQ, ICAT, SILAC etc). A Shimadzu Prominence 1D nano-LC system is used to provide upstream separation of samples with reverse phase chromatography. 
The QTRAP 5500 mass spectrometer is a quadrupole-TRAP instrument most suitable for quantification of samples and structural analyses (eg MS^3, neutral loss and precursor ion scans). It has at least 10-fold sensitivity over previous models. An Agilent 1100/1200 capLC and a Shimadzu UHPLC system are available for upstream separation of samples.
The Voyager is a robust instrument that requires minimal training for running samples. Its primary use is in mass measurement of intact molecules (eg, polymers, intact proteins) as well as mass fingerprinting, in which a protein is identified by accurately measuring the masses of its proteolytic (usually tryptic) peptides followed by database searching for protein identity.

Sample Requirements

Sample preparation is critical and needs to be detergent free and ideally salt free.

In general, for protein identification and quantification, samples need to be enzymatically digested (eg trypsin) followed by SPE (solid phase extraction) cleanup. Amount depends on sample complexity with sensitivity on the order of femtomol to attomol range.  However as an easy guide, a Coomassie stained gel slice should provide excellent results.  An offline capLC system is available for upstream factionation of complex samples.

For intact mass analysis, proteins need to be in a detergent free buffer or solvent. Amount required depend on size: 
  • 5 kDa:  ~25 pmol
  • 20 kDa:  ~100 pmol
  • 60 kDa:  ~500 pmol


For further information, advice on sample prep, or experimental design contact:

Dr Amanda Nouwens
3346 9490

Note: researchers will need to undertake the relevant building and other inductions prior to using equipment in the facility without supervision.


To cover consumable and maintenance costs of the instruments an access fee is in place.
MS charges 2014 (applicable to UQ users):
Individual analyses: $200 / sample (NB: if more than 20 samples within 12 months, pricing converts to tier charges).


Tier 1 group user
Up to 400 samples or up to 300 hrs
$4000 / yr or $2000 / 6 months (at half the usage rate).
Tier 2 group user
401-800 samples or 300 – 600 hrs
$7000 / yr or $3500 / 6 months (at half the usage rate).
Tier 3 group user
801-1600 samples or 600 – 1200 hrs
$10000 / yr or $5000 / 6 months (at half the usage rate).
For usage above 1600 samples (or 1200 hrs annually), price by negotiation.
(NB Tiers are based on sample number and hours as some samples require long acquisition times).
Fees for users external to UQ are available on application.  UQ users have priority of access to the facilities.


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