Mass spectrometry


Mass Spec at the BRF

The ACRF BRF maintains an AB MDS Sciex 4800 MALDI-TOF-TOF Mass Analyzer.  In  the TOF mode this instrument is useful for the characterisation of large molecules, especially polymers and biopolymers such as proteins and nucleic acids, some classes of lipid and carbohydrate.  These molecules may be subjected to collision-induced-dissociation in the TOF-TOF mode enabling classical applications such as peptide and protein identification subsequent to tryptic digestion.

Other Mass Spec services on campus

The Mass Spectrometry Facility (MSF) at the Research School of Biology provides a campus-wide service to researchers who need to identify and quantify metabolites and proteins (bottom-up proteomics following a tryptic digest).  For this purpose we are equipped with a quadrupole GC/MS (EI/CI), an iontrap GC/MS (EI/CI) and a LC-QTOF MS/MS (ESI).  To assist with sample preparation the MSF also houses an OffGel Electrophoresis Fractionater for complex protein/peptide samples and an HPLC system equipped with UV/Vis, Fluorescence and Evaporative Light Scattering Detectors.
The MSF is run by Dr Charles Hocart and Dr Thy Truong.

MSF website (


Service Summary

  1. Samples pre-spotted by user on 384 plate.  Digestion and analysis undertaken by user.  Results as .ppw file.
  2. Service includes protein digestion, desalting, concentration, MS data acquisition, Mascot database searching and standard report.  Cost of plate not included.
  3. Mass analysis of intact protein.
  4. De Novo peptide sequencing is an additional data analysis service based on data acquired from MALDI-TOF/TOF.  Price is inclusive of all work as per (2).
  5. Reduction and alkylation of samples is recommended.  Spots submitted from 2D gels are usually alkylated and do not require additional alkylation steps.


  Services ANU External non-profit External commercial
1 Pre-spotted samples for MALDI-TOF/TOF analysis (per run 73-96 samples on a 384 plate) $500 $750 $1000
  Pre-spotted samples for MALDI-TOF/TOF analysis (per run 49-72 samples on a 384 plate) $375 $560 $750
  Pre-spotted samples for MALDI-TOF/TOF analysis (per run 25-48 samples on a 384 plate) $250 $375 $500
  Pre-spotted samples for MALDI-TOF/TOF analysis (per run 1-24 samples on a 384 plate) $125 $180 $250
2 MALDI-TOF/TOF for protein identification (per sample) $100 $150 $200
3 Phosphorylation screen (per sample) $100 $150 $200
4 Intact Mass Determination (per sample) $100 $150 $200
5 De Novo peptide sequencing (per sample) $100 $150 $200
6 Reduction adn alylation (per sample) $100 $150 $200
7 1D nanoLC-MALDI-TOF for protein identification Please contact BRF Please contact BRF Please contact BRF
8 2D nanoLC-MALDI-TOF for protein identification Please contact BRF Please contact BRF Please contact BRF


Order form

A mass spectrometry order form can be downloaded.

Mass Spectrometry Analysis request form (PDF 68KB)

Terms & conditions


  1. The BRF operates on a cost recovery basis.  The percentage of subsidization is determined by The John Curtin School of Medical Research.

  2. No samples or orders will be processed without an authorised* sample submission/order form and valid charge code.

 (*Authorised by signature of the PI/Lab Head, or by granting of electronic access to BRF ordering systems with the authority of the PI/Lab Head).
  3. It is a condition of the contract between the ACRF and JCSMR/ANU that "the Foundation (ACRF) is to be acknowledged in all scientific publications which utilise the Facility (BRF) at the Institute (JCSMR)".  
All work performed in the BRF, whether full service or not, and the use of any BRF resources should be acknowledged in all publications arising from that work.This should be in the “Material and Methods” section of the paper (see examples in the column to the right). Any further individual acknowledgements are solely at your discretion.

A reference to the publication should be sent to the Manager of the BRF once the paper is published (includes theses).

BRF collaborations and co-authorship:  although the BRF is primarily a service unit, there are instances where BRF staff make significant contributions to either the technical or intellectual input of the project. This should be discussed with the staff member concerned prior to commencement of the collaboration. 

Consumables and data


The customer agrees to cover the cost of any consumables ordered on their behalf if the customer fails to supply the correct quantity and quality of the starting material required for processing.  Details of the quality and quantity required are on the BRF website and sample submission form. 

  2. Customers are responsible for archiving data generated by the BRF. Data generated by the BRF are solely for the use of the customer and their collaborators.  Data is not to be sold to a third party. 

 The BRF shall not be responsible for data output generated from samples that deviate from recommended protocols as requested by the customer.

  3. Upon receipt of consumables and/or data, the customer accepts responsibility for the correct handling, use, storage and disposal of the consumables/data.
  4. The BRF extends no warranties of any kind in respect to the consumables.

  Any consumables sold may have hazardous properties.  The customer agrees to use appropriate caution and safeguards as not all properties are known. 

  5. Consumables sold by the BRF shall not be transferred to another party without the written consent of the BRF.  The BRF is not responsible for any losses arising from the use of consumables.  

The BRF will not be liable to the customer for any loss, claim or demand made by the customer due to acceptance, handling, use, storage or disposal of consumables and/or data by the customer, except to the extent permitted by law when it is the result of wilful misconduct on the part of the BRF or its employees.

Acknowledgement in Publications


Real-time PCR

“Amplifications were performed in 384-well optical reaction plates (Applied Biosystems) with a 7900HT Fast Real-Time PCR System at the ACRF Biomolecular Resource Facility, The John Curtin School of Medical Research, Australian National University, using SDS 2.4 software to analyse raw data.”

DNA Sanger Sequencing

“Amplified PCR products were purified and sequenced on an AB 3730xl DNA Analyzer (at the ACRF Biomolecular Resource Facility, The John Curtin School of Medical Research, Australian National University) following the manufacturer's protocol (Applied Biosystems 2002).”

Peptide synthesis

“Peptides were synthesized chemically using the 9-fluorenylmethyloxycarbonyl (Fmoc) method on a CEM Microwave-assisted Peptide Synthesizer and purified by one round of C18 reversed-phase HPLC by the ACRF Biomolecular Resource Facility at the John Curtin School of Medical Research, Australian National University. As required, the N- or C-terminus, or both, were protected by acetylation or amidation, respectively.” 

Tetramer synthesis

“Cells were surface stained with APC-labelled tetramers consisting of murine class I MHC molecule (H-2Db), b2-microglobulin and influenza nucleoprotein peptide NP366–374. Tetramers were synthesised at the ACRF Biomolecular Resource Facility at The John Curtin School of Medical Research, Australian National University using BirA enzyme synthesized as described (O’Callaghan et al., 1999). [O’Callaghan, C.A., Byford, M.F., Wyer, J.R., Willcox, B.E., Jakobsen, B.K., McMichael, A.J. and Bell, J.I (1999). BirA Enzyme: Production and Application in the study of membrane receptor-ligand interactions by site-specific biotinylation. Anal. Biochem. 266, 9-15.]”

Updated:  26 September 2018/Responsible Officer:  Director, ACRF/Page Contact:  Web Admin, ACRF