FCUL houses a state of the art FTICR mass spectrometer, a Bruker Apex Ultra (Billerica, U.S.A.) with a 7 Tesla actively shielded magnet from Magnex, Oxford U.K.


The instrument is equipped with an Apollo II dual source, capable of simultaneous ESI and MALDI ionization modes. Each mode can also be used individually.

Ion optics is Qh type and the quadrupole can be used as a collision cell and m/z selector/accumulator. The ICR cell is a cylindrical, infinity type. Gated and Side-Kick trapping modes can be used. A hollow cathode is installed. Two leak and two pulse valves are also installed.


Mass accuracy. Better than 2 ppm with external calibration, better than 1 with internal calibration

Resolution. About 1 million in narrowband-mode. About 50-100 thousand in routine broadband mode.

m/z Range. Nominal range is 10-10000. In practice, the best results are obtained in the range 200-4000. Above 4000, the quadrupole only works in rf transmission mode (no selection and no fragmentation). Range is ideally suited for proteomics work


ESI and nano-ESI modes can be used, at flows up to 10 microL/min and 1 microL/min, respectively.

The MALDI source uses standard Bruker target plates. Best results are obtained with anchor-chip targets with DHB matrix.

Methods available

Exact mass for molecular ions, from low to high molecular masses. Isotopic resolution for proteins up to 66 kDa.

High accuracy and resolution peptide mass fingerprinting for both MALDI and ESI ionisation modes for tryptic digest. From purified proteins to complete proteomes.

Identification and location of post-translational protein modifications

Top-down protein analysis, including sequencing, identification and location of post-translational modifications.


CID (Collision induced dissociation). This is the most common method, whereby ions are selected, accelerated and collides with an inert gas, like argon. For the collision energies available, it requires double charged species and is ideally suited for LC-MS methods or ESI ionisation. For peptides, it produces b and y ions.

ICR Cell

SORI-CID (Sustained off-ressonance collision induced dissociation). This method is unique to FTICR mass spectrometers. Once in the ICR cell, ions are selected and continuosly excited and de-excited, accumulating energy. By pulsing an inert gas in the cell, collision occur and the ions fragment. Useful for just about any ion, particularly, the ones produced by MALDI. Thus, it offers the possibility to sequence peptides, producing b and y ions.

ECD (Electron capture dissociation). Again, a unique method for FTICR mass spectrometers. Multiply charged ions are irradiated with electrons in the gas phase and dissociate. Forpeptides, it produces c and z ions. Ideally suited to multiply charged ions such as large peptides and proteins.

MS n

n = 3, tested up to n = 6

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