TripleTOF 6600

Mass Spectrometer




The TripleTOF 6600 is ideal for identifying, characterising and quantitating proteins and peptides, especially in complex mixtures, or where sample amount is limited.

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The TripleTOF 6600 is a versatile instrument with high sensitivity, speed, and productivity in a single multifaceted platform to help you dig deeper into complex samples. Ultra-fast acquisition rates allow you to collect high-resolution MS/MS data on every detectable analyte in your sample, giving you the potential you need to advance your research. It is ideally suited for protein identification, PTM analysis, quantitative global proteomics, protein MW analysis. Multi-dimensional chromatography (e.g. Strong Cation Exchange (SCX) coupled with reversed phase) enables in-depth analysis of complex samples, while advanced techniques (SWATH, iTRAQ, sMRM HR, and ion mobility separation) allow you to get the most information out of your sample.

This instrument has state-of-the-art features including SWATH Acquisition for comprehensive proteomic analysis, and high resolution Multiple Reaction Monitoring (MRM-HR) for accurate quantitation of peptides in highly complex samples. This system also features the Selexion ion mobility interface to allow the separation of different classes of analytes, resolution of structural isomers, reduction of background signals to improve sensitivity, and gas phase fractionation of complex mixtures. With a dynamic range in excess of five orders of magnitude and up to 200 MS/MS events per second, this is our most powerful instrument for proteomic applications.



      • Mass Range: 5-40,000 m/z
      • Mass Selection Range: 5-2250 m/z
      • Mass Accuracy : 2 ppm
      • Mass Resolution: ≥35,000 (FWHM) at 956 m/z
      • Nano/capillary LC and NanoESI
      • 4-channel MCP detector with ADC signal processing for extended dynamic range


Analysis for the TripleTOF 6600 is supported by the following software:

  • ProteinPilot
  • PeakView
  • MultiQuant
  • MarkerView
  • Skyline

Access to the above software is available in the analysis suit or via the  Proteomics Virtual Machine. Contact Martin Middleditch for more information.


Email Martin Middleditch for all enquiries related to the TripleTOF 6600 MS.


  • Sample preparation protocols for each project should preferably be discussed beforehand for quality data analysis.
  • Sample preparation involving serum albumin should be avoided where possible as the albumin can suppress other scarce proteins/peptides.
  • While LC-MS does deal with some level of salts, it is best to minimise concentrations of non-volatile buffers.
  • It is best if no detergents are used during sample prep, or extensive steps taken to massively reduce their concentration in the final extract.
  • This instrument is not housed in a PC1 area and only non-hazardous samples are allowed to be transported to and analyzed in the laboratory.


  • This instrument is run primarily by centre staff for analysis services. It is not currently available for self use.
  • Protein identification and quantification can be compromised if the sample preparation and processing are inadequate.
  • Data analysis can be complex and time-consuming depending on the application.
  • The instrument is set up for nanoflow chromatography. -CID is the only fragmentation process available.


The cost varies depending on task and support level required. Current user costs are listed in iLab booking system.

Service Cost
Infusion MS $60.00
Infusion MS/MS $90.00
30min LC-MS/MS (Discovery-type) $125.00
60min LC-MS/MS (Discovery-type) $175.00
90min LC-MS/MS (Discovery-type) $225.00
MRM(Targeted-type) $60.00



Available for postgraduate students, doctoral candidates and staff of the University of Auckland. External users and commercial users are also eligible to use the equipment.

Access Requirements

The TripleTOF6600 is housed on the Main Campus in the School of Biological Sciences.


This instrument is operated by staff only.


Users can request analysis on the TripleTOF through ou iLab booking system. Users and their principal investigators or research group need to first have accounts in the iLab booking system. Contact Martin for more details.