Mass spec instrumentation

• Two main advantages of using mass spectrometry over other structural analysis techniques:

  • Can obtain structurally sensitive data from very small samples - from 1 femtomole of material (1 x 10-15 moles)
  • Can analyse highly complex mixtures of biological material - not limited to proteins, but polysaccharides, lipids etc
• Three basic parts of a mass spectrometer:

  • Ion source - most biological samples are not ionised already and neither are they in the gas phase, so ionisers are responsible for this.
  • Mass analyser - determines the mass/charge ratio of the ions in the mixture. Misleading name!
  • Detector - collects quantitative data on the mass/charge ratio of the mixture. Could analyse whether the abundance of a particular protein or peptide varies with the addition of a drug
• In hard ionisation techniques, lots of energy is needed to get the molecules to enter the gaseous ion state, therefore often an excess of energy which causes fragmentation of ions
• In soft ionisation techniques, there is just enough energy in the ionisation system that ions are converted to the gas phase, but this is not enough to cause fragmentation
• Electron impact ionisation is a hard ionisation technique, so generates fragment ions.
• Electrospray and MALDI ionisation are soft ionisation techniques so tend to only produce molecular ions
• If you were doing a MS study to determine protein sequence, you'd use electrospray or MALDI to generate peptides and electron impact to generate fragments from the peptides that can be sequenced
• Electron impact ionisation produces positive, singly charged radical cations
• Electrospray ionisation produces positively OR negatively charged ions that can be singly or multiply charged
• MALDI produces positively or negatively charged, singly charged ions
• Electron impact ionisation has a molecular weight limit of 1 kDa
• Electrospray ionisation has a molecular weight of >500 kDa
• MALDI has a molecular weight limit of 500 kDa
• Electron impact ionisation is carried out on gas phase samples
• Electrospray ionisation is carried out on liquid phase samples
• MALDI is carried out on solid samples
• Electron impact ionisation generates ions by knocking off a proton
• Process of electron impact ionisation:

  1. Sample in gas phase gently heated to bring it into the focus of the electron beam. Electrons are emitted from a tungsten or rhenium filament.
  2. Electron beam comes close enough into proximity of outer orbital electron that the negative charge of the electrons repels each other
  3. This causes ejection of the outer orbital electron from the molecule to generate radical cation
  4. Ion repeller has high negative charge to eject the radical cations from the ion source into the mass analyser.
• The key three factors that define a good mass analyser:

  1. Upper mass limit - what is the biggest ion that can be separated out depending on its m/z ratio?
  2. Ion transmission - how many ions in the sample will be detected?
  3. Resolution - how good is the mass analyser at separating ions with very similar m/z ratios?
• Quadrupole set up:

  • Four magnetic poles - two neg charged, two pos charged, connected electrically.
  • Strength of the electric field generated by the quadrupole can be varied - vary the strength and create a calibration curve to determine the m/z ratio.
  • Ions enter the quadrupole from the ionisation source and flow through to the detector at the other end of the quadrupole.
• Resolution of MS data collected from the quadrupole is restricted as ions are lost during the process: only ions that are resonant with the electric field hit the detector, the rest get annihilated as they collide with the quadrupole.
• The m/z limit of a quadrupole is approx 4000
• Advantages of using a quadrupole:

  • Low cost
  • Rapid scanning
  • Ideal for gas chromatography mass spectrometry i.e. paired with electron impact ionisation
  • Widely used for electrospray MS
• In ion trap analyser, ions are trapped in a closed chamber. Ions with a selected m/z range are ejected after RF voltages are scanned. Mass spectrum is produced by scanning RF voltages to eject ions through an end cap.
• In orbitrap mass analyser, ions are trapped by static electrostatic field orbit around central electrode and

  oscillate in an axial direction. Frequency of axial oscillation relates to m/z via a Fourier transform.
• In orbitrap, varying the field strength changes the speed of rotation and thus influences the frequency of axial oscillation
• Orbitrap analysers have high mass accuracy and therefore are high cost
• Time of flight mass analysers separate ions by differences in velocity - low m/z generates the highest velocity
• In time of flight mass analysers, reflectrons correct for kinetic energy distributions and reduce peak broadening. Ions with more energy travel further into the reflectron before being repelled, thus giving all the ions the same energy so they can be detected according to velocity alone
• In general, the mass analysers from worst to best:

  • Quadrupole
  • Ion trap
  • Orbitrap
  • Time of flight
• There are three types of ion detectors:

  • Photomultiplier (PM): ions strike dynode, causing electron emission. Electrons strike phosphorous screen, releasing photons. Photons enter multiplier where they are amplified and detected.
  • Electron multiplier (EM): ions strike dynode, causing electron emission. Amplification when they next strike dynode
  • Micro-channel plate array detectors (MCP): simultaneously detect multiple m/z values
• Most commonly, electron impact ionisers are paired with quadrupole analysers as this is the cheapest method
• Electron impact ionisation requires molecules to be volatile, i.e. low molecular weight and non-polar
• MALDI sources are most commonly found on instruments with time of flight analysers
• Hybrid instruments such as MALDI TOF/TOF analysers tend to be used for MS/MS experiments, e.g. peptide sequencing
• Process of electrospray ionisation:

  • Sample introduced through hyperdermic needle coated with gold/palladium.
  • High voltage (3-4 kV) is applied as needle introduced to electrode
  • Sample dispersed as an aerosol of highly charged droplets.
  • Drying gas causes solvent to evaporate, so droplets become smaller
  • Similarly charged ions are brought closer together; their repulsion causes droplets to explode, forming smaller ones.
• Nano-electrospray ionisation is an adaptation that improves the flow rate and sensitivity
• MALDI:

  • Sample co-crystallises with matrix
  • Matrix absorbs energy from laser and transfers it to sample, causing ionisation
• In MALDI, delayed extraction ensures well resolved spectra are generated. The pulse of ions is kept in the source for a short time after the laser pulse to allow ions formed deep in the matrix to emerge and catch up with those formed near the surface
• Common MALDI matrices:

  • Alpha-cyano-4-hydroxycinnamin (for peptides and proteins)
  • 2,5-dihydroxybenzoic acid (2,5-DHB) for carbohydrates