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Biomolecule Mass Measurement

The masses of molecules of interest (proteins/peptides, oligosaccharides, lipids or nucleic acids) can be determined with high accuracy using mass spectrometry. The size of a known protein or peptide can be confirmed or the extent of its modification (proteolytic, post-translational or chemical) determined. Mass profiles of biological fluids can be made.

Sample Preparation

  • The sample should be in soluble form and free of detergents.
  • Desalting by reversed phase chromatography (on-line or off-line) is often necessary.


ESI-MS (generates multiple charge states of proteins)

LTQ Orbitrap XL ETD (Thermo Fisher Scientific)

  • Sample is introduced via flow injection or syringe pump.
  • Accurate to within 50-100 ppm for proteins
  • Resolution near theoretical limit of isotopic envelopes

MALDI-TOF (generates singly or doubly charged forms of most proteins)

Ultraflex III and UltrafleXtreme (MALDI TOF/TOF, Bruker Daltonics )

  • Sample is mixed with matrix on a target plate and may be desalted on the target
  • Accurate to within 150-300 ppm for proteins
  • Resolution ¼ - ½ of the theoretical limit of isotopic envelopes
  • Can be highly sensitive
  • Can generate profiles from biological fluids in a single analysis
  • Highly accurate (better than 10 ppm) for the measurement of peptides of mass < 4 kDa

Data Analysis

ESI-MS: masses are calculated by mathematical transformation of the m/z ion series.

MALDI: Masses of the analytes are normally observed directly.


A written report is provided, describing the analysis undertaken and masses measured. Where appropriate, comparisons with calculated masses are made. Raw data are in proprietary formats and are not included with the report. Data are archived by the APC for at least 12 months or according to customer's requirements.

Adelaide Proteomics Centre

Level 1
Molecular Life Science Building
The University of Adelaide
SA 5005

Location and map


T: +61 8 8313 5497