The linear ion trap is an extremely fast but low resolution and low mass accuracy mass analyzer (+/- 0.5 m/z typical accuracy). This type of mass spectrometer confines and manipulates ions through the use of quadrupolar radio-frequency (RF) fields. Linear ion traps are extremely flexible and are used for collisional dissociation (a process used to 'sequence' peptide ions), ion-ion interactions, and ion storage prior to higher resolution mass analysis. Series of linear ion traps can even be strung together to create more flexible mass spectrometers, as in the Velos mass spectrometer present in our laboratory. We have one "stand-alone" linear ion trap at the Broad Institute but have several more that are coupled to higher resolution mass spectrometers in "hybrid" instruments.
The Orbitrap is a high resolution mass analyzer with high mass accuracy (+/- 5 part-per-million m/z). In practice, the Orbitrap analyzer is the second stage of a hybrid mass spectrometer whose first stage is typically a linear ion trap. Ions are injected into the Orbitrap tangentially and form oscillating rings around the central electrode, becoming trapped in an electrostatic field. The frequency of axial oscillation can be related by Fourier transform to the mass-to-charge ratio (m/z) of the ion. The Proteomics Platform utilizes 5 Orbitrap mass spectrometers: three LTQ-Orbitraps, one LTQ-Orbitrap XL, and one LTQ-Orbitrap Velos.
Like a linear ion trap, a triple quadrupole mass spectrometer uses RF fields to manipulate ions. In this case, ions form a continuous beam rather than being stored in a trap. As the name implies, there are three quadrupoles. The first (Q1) and the third (Q3) quadrupoles are very similar as they serve to identify and filter different masses while the second quadrupole (q) serves as a collision cell. In the collision cell the masses will undergo collision-induced dissociation (CID) which fragments the peptide into smaller ions. A triple quadrupole mass spectrometer allows the user to monitor one or more “precursor” masses in Q1 as well as the fragment ions related to each precursor mass in Q3. The precursor mass is the mass of the peptide, typically in the +2 or +3 charge state, before it undergoes CID. By monitoring for both the precursor mass of a particular peptide and one or more fragment ions of the same peptide, it is possible to determine the presence of the peptide, even in a complex solution. The triple quadrupole is the type of instrument used for multiple-reaction monitoring (MRM) quantification assays. The Broad Institute has 4 triple quadrupole instruments for proteomics experiments.
Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is a high resolution / high mass accuracy technique that shares many properties of the Orbitrap. Ions become trapped in a high strength magnetic field where each ion has a characteristic "cyclotron" frequency of oscillation that can be related to its mass-to-charge ratio. The FTICR-MS measures m/z by detecting the cyclotron frequency produced by the trapped ions. Moreover, the ions can be maintained in the trap for long periods (several seconds), allowing for the frequency to be read multiple times, which makes the FT more precise. A mass spectrum is extracted from the signal data using a Fourier transform, a mathematical function. Advantages of an FT are its high sensitivity and high resolution, but its operation is relatively slow and it requires frequent maintenance. The Broad Institute has one FTICR-MS hybrid instrument with a 7 Tesla superconducting magnet.