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Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

The Agilent 6540 UHD accurate-mass quadrupole time-of-flight (Q-TOF) mass spectrometer is an accurate mass MS/MS instrument based upon quadrupole and time-of-flight technology. The Agilent 6540 Q-TOF can deliver exceptional sensitivity, dynamic range, isotopic fidelity, mass accuracy and resolution to meet your most challenging research needs.

Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

Figure 1. The Agilent 6540 UHD Accurate-Mass Q-TOF mass spectrometer

The Structure of Agilent 6540 Q-TOF Mass Spectrometer

As shown in Figure 2, the Agilent 6540 Q-TOF mass spectrometer consists of an ion source, the ion optics, quadrupole, collision cell, ion beam shaper, TOF mass analyzer, and ion detection.

Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

Figure 2. Schematic of Agilent 6540 UHD Accurate-Mass Q-TOF LC/MS

Ion Source

In the ion source, the sample is ionized. This instrument contains several atmospheric pressure ionization sources, including electrospray ionization (ESI), chemical ionization (APCI), and JetStream ESI. As shown in Figure 3, the JetStream ESI, ESI with Agilent Jet Stream Technology, uses super-heated nitrogen sheath gas to confine the electrospray. Ion density and desolvation are improved, leading to higher MS signal intensities and reduced noise. The MS and MS/MS sensitivity can improve 5 to 10 fold by Agilent Jet Stream technology at optimal LC flow rates.

Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

Figure 3. ESI with Agilent Jet Stream Technology

Ion Optics

Ion optics contain skimmer, octopole ion guide, and lens. Sample ions produced in the ion source are electrostatically drawn through a drying gas and then pneumatically conducted through a heated sampling capillary into the first stage of the vacuum system. The skimmer can deflect the majority of drying gas and solvent vapor. After passing through the skimmer, the ions pass into the octopole ion guide, where the ions are immediately focused. An octopole ion guide is a set of small parallel metal rods with a common open axis.


The quadrupole, consisting of four parallel metal rods, works as a mass filter. Only selected m/z ions can pass through the rods while other ions will collide with the rods. The hyperbolic rods can optimize ion transmission and spectral resolution. The end section of the quadrupole also consists of short hyperbolic rods, but their radio frequency (RF) voltages are only high enough to guide ions into the collision cell.

Collision Cell

Collision cell, where the selected ions are fragmented, is a high pressure hexapole assembly with its axial acceleration adjusted to maximize sensitivity while eliminating crosstalk. A collision energy voltage is applied over the accelerating linear voltage to generate fragments or product ions. The hexapole assembly is small diameter, helping capture fragmented ions. The geometry of a hexapole offers advantages in ion focusing and ion transmission. The collision cell is comprised of six resistively coated rods that are used to produce a potential difference across the length of the collision cell. In this way, precursor ions or fragment ions are transmitted and not allowed to drift around at random.

Ion Beam Shaper

The ion beam shaper provides 10-fold compression and cooling to create a denser and thinner ion beam that passes through a narrower slit leading into the slicer and pulser region. To facilitate ion beam shaping, lenses focus the ions, so the ions will enter the TOF analyzer as a parallel beam. The more parallel the ion beam, the higher the resolution in the resulting mass spectrum.

Time-of-Flight Mass Analyzer

The nearly parallel beam of ions passes into the ion pulser of TOF. A high voltage (HV) is applied to the ion pulser to start the flight of the ions to the detector. The ions leave the ion pulser travel through the flight tube, which is about one meter in length. At the end of the flight tube, there is an ion mirror, called reflectron, which reflects the ions near the end of the flight tube. The reflectron increases the resolving power of the instrument by effectively doubling the flight distance in the same space, and by performing a refocusing operation so that ions having different initial velocities still arrive simultaneously at the detector.

Ion Detection

Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

Figure 4. Ion detector of Agilent 6500 Q-TOF series.

The ion detect contains a microchannel plate (MCP), a scintillator, and a photomultiplier tube (PMT). When ions hit the front surface of the MCP, an electron escapes and begins the process of electrical signal amplification. Then, these ions are focused onto a scintillator that can produce a flash of light when struck by electrons. The light produced by the scintillator passes to the PMT with a signal output at ground potential.

The Principle of Q-TOF Mass Spectrometer

Agilent 6540 UHD Quadrupole Time-of-Flight Accurate-Mass Mass Spectrometer

Figure 5. A) Schematic diagram of the quadrupole mass analyzer and B) Reflector TOF analyze

The quadrupole mass analyzer can separate ions according to their mass-to-charge ratios (m/z) by using the stability of the trajectories in oscillating electric fields. As shown in Figure 5A, it consists of four parallel metal rods, and radio frequency (RF) voltage with a DC offset voltage is applied between one pair of rods and the other. It can work as a mass filter to transmit only ions of a selected m/z value to achieve a stable trajectory. Ions with other m/z values collide with the rods or walls and cannot pass the rods.

As shown in Figure 5B, the derivation process clearly reveals that the time of flight of ions varies with the square root of m/z in the linear TOF. Therefore, under the ideal state, the lighter ions will arrive earlier at the detector than the heavier ions. In Agilent 6540 Q-TOF mass spectrometer, the reflectron TOF analyzer, consisting of a series of ring electrodes with high voltage, can correct the kinetic energy distribution in the direction of ion flight and increase resolution. The ions with more energy penetrate deeper into the reflectron, while the less energetic ions of the same m/z penetrate a shorter distance into the reflectron. In that way, the detector receives ions of the same m/z at (about) the same time.

Working Mode of Agilent 6540 Q-TOF Mass Spectrometer

TOF Mode

The Quadrupole is under the situation of Total Transmission Ion (TTI), which means all ions can pass the quadrupole. The collision cell does not fragment the ions and works as ion transmission devices. The TOF mass analyzer is in the scan mode and can directly detect the ions. The mass spectrum obtained from the TOF mode is equivalent to the one from the single TOF mass analyzer.

Auto MS/MS Mode

In this mode, the instrument can automatically perform secondary mass spectrometry on qualified ions according to the conditions set by users. When a particular ion or a set of ions meet the set conditions, the quadrupole is in the selected ion monitoring (SIM), and the collision cell can fragment ions. Then the fragment ions can be scanned by TOF and get a mass spectrum. The auto MS/MS mode is commonly used for unknown compounds identification and structure analysis.

Targeted MS/MS Mode

In this mode, only the ions targeted by users can get mass spectrum. Similar to the auto MS/MS mode, the quadrupole is in SIM, and the collision cell can fragment ions. Then the fragment ions can be scanned by TOF and get a mass spectrum. This mode is useful for the quantitative analysis, identification of known compounds, and structural elucidation.


  • Powerful Data Mining and Analysis Capabilities. The MassHunter software of Agilent makes mass spectrometry analysis faster, simpler, and more efficient. A sophisticated algorithm can automatically retrieve all information for each component, including overlapping and co-eluting peaks, so saving hours of analysis time. In addition, MassHunter software can use public and software database for automated and accurate searches to make compound identification easier. Pesticides, forensics, toxicology, and other small molecule compounds can be screened and identified using a chemical formula generated from accurate mass MS or MS/MS data and an accurate mass and retention time database.

  • Clearly better performance. The Agilent 6540 Q-TOF with Ion Beam Compression (IBC) and Enhanced Mirror Technology (EMT) can improve mass accuracy and resolution. The IBC compresses and cools the ion beam into a very dense layer of ions for enhanced mass resolution and mass accuracy with minimum sensitivity loss. In addition, as mentioned above, the Agilent Jet Stream technology can improve sensitivity performance.

The Agilent 6540 UHD Accurate Mass Q-TOF with Agilent Jet Stream technology, IBC, EMT, and MassHunter Workstation data mining tools can provide sensitive, accurate-mass MS and MS/MS analyses with high resolution. The exceptional MS and MS/MS performance enables the 6540 Q-TOF system to support demanding applications, including protein/peptide identification and characterization, metabolomics, biomarker discovery, impurity profiling, compound profiling, natural products screening, and combinatorial chemistry target compound analysis. At Creative Proteomics, we can provide a wide range of reliable services by using Agilent 6540 UHD Accurate Mass Q-TOF mass spectrometer to support your research.

* For Research Use Only. Not for use in diagnostic procedures.
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