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LTQ Orbitrap MS Small Molecule / Peptide Mass Measurement

Compound masses can be measured with high resolution and high mass accuracy using the LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific). Accurate mass measurement allows for calculation and elucidation of the elemental composition. The high resolution is necessary to separate ions that are interfering (eg same nominal mass, but different fractional masses).

The mass spectrometer can be used with an ESI source or nanoESI source which can accommodate for flow rates from 100 nL up to several 100 uL, as well as offline nanospray.

The instrument is capable of MSn experiments (several fragmentation modes are possible, eg CID and ETD).

Sample Preparation

  • The sample should be of high purity.
  • Any ionisable impurity may suppress ionization of the compound of interest and therefore poor quality spectra may result and elemental composition may not be possible to determine.
  • Samples can be submitted as solids or in solution using an appropriate solvent, an accurate amount and concentration of the sample must be provided. It is necessary that a low percentage of acid will be added to the sample prior to measurement.


LTQ Orbitrap XL

  • Sample introduction by ESI or nanoESI, using a syringe pump or flow injection
  • Offline nanospray is also available using coated glas needles (for up to 10 uL sample)
  • Masses accurate to within 2 ppm for most compounds
  • Resolution better than 60 000 at m/z 400 at 1 scan/second
  • Mass range 50-2000 or 2000-4000
  • Fragmentation CID, PQD or ETD
  • positive and negative ionisation possible

Data Analysis

The masses can be compared with a theoretical spectrum of the compound of interest. The elemental composition can be elucidated.


A written report is provided, describing the analysis undertaken and masses measured. Comparisons with theoretical masses are made. Raw data are not included in the report. Data is 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