Used Mass Spec in Mass Spectrometry

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  • Agilent G6538A 6538 UHD Accurate-Mass Q-TOF LC/MS

    Mass Spec

    BSIID: 8003728

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  • Waters Micromass ZQ

    Mass Spec

    BSIID: 2035717

    Price: $4500.00

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  • Perseptive Biosystems Voyager-DE BioSpectrometry Workstation

    Mass Spec

    BSIID: 2035337

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Elucidating the power of mass spectrometry

Mass spectrometry is an indispensable technique used to analyze biomolecules. From analysis of glycans, lipids, proteins, peptides, to oligonucleotides, a mass spectrometer can help clarify the structure and chemical properties of different molecules.

A mass spectrometer is an instrument that measures the masses of individual molecules that have been converted to ions or molecules that have been electrically charged. This instrument helps scientists identify molecules in solids, liquids, and gases. It is also used to determine the quantity of each type of molecule in a mixture as well as which atoms comprise a molecule and how they are arranged.

Main Components

A mass spec is composed of three main parts:

  1. Ion Source – ionizes chemicals or compounds to generate charged molecules or fragments.
  2. Mass Analyzer – takes the ionized chemicals or compounds and separates them based on charge to mass ratios.
  3. Ion Detector – detects the presence of the ionized chemicals or compounds in the air and recording their quantity.

Below are the basic steps for mass spectroscopy:

  1. Ionization – Molecules must be charged in order to be measured by a mass spectrometer. So the first step in mass spectrometry is ionization. Ionization occurs when an atom’s electron or electrons is removed to give a positive ion (mass specs always work with positive ions). This is done by introducing the molecules into a high vacuum tube system where the particles are collided with a beam of high speed electrons. Note though that if samples are not already a gas, they must be vaporize and in a free moving gaseous form.
  2. Acceleration – The ionized molecules are accelerated down a tube (from + to – plates) and then through a very strong magnetic field in order to produce the same kinetic energy.
  3. Deflection – The tube is surrounded by a curved magnetic field that causes the cation to be deflected in proportion to its mass-to-charge ratio (m/z). The magnetic field can be varied to change the path of deflection. It is the molecular mass, charge, and strength of the magnetic field that determines the flight path or deflection path of the ion.
  4. Detection – the ion detection system generates small electrical currents when the ions hit it.


There are several different types of ion sources used for different analytical instruments and applications. Below are a few sources to choose from:

Ionization Sources Description
Electron Ionization (EI) Used for small (less than 600 mw) neutral organic molecules that do not easily decompose.
Chemical Ionization (CI) Used when no molecular ion is observed in EI mass spectrum of a compound.
Electrospray Ionization (ESI) Used for molecules that have a tendency for fragmentation. Can produce multiply charged ions.
Atmospheric Pressure Chemical Ionization (APCI) Used for generating ions directly from solution and is capable of analyzing relatively non-polar compounds.
Matrix Assisted Laser Desorption/Ionization (MALDI) Used for biomolecules and large organic molecules which tend to be fragile. Similar to ESI, but produces fewer multiply-charged ions.


Each mass analyzer has its own special characteristics and application, along with benefits and limitations. Choosing a mass analyzer should be based on application, cost and performance desired. Below are 4 general types of mass analyzers that can be used to separate ions along with a few guidelines on each:

Mass Analyzer Benefits Limitations Applications
Double focusing Magnetic Sector
  • Classic mass spectra
  • High reproducibility,
  • High resolution and sensitivity
  • Not suited for MALDI
  • Larger
  • Higher cost
  • All organic MS analysis methods
  • Accurate mass measurements
  • Isotope ratio measurements
Quadropole Mass
  • Classical mass spectra
  • Good reproducibility
  • Small
  • Lower cost
  • Limited resolution
  • Not suited for MALDI
  • Peak height vs. mass must be tuned
  • Most benchtop GC/MS and LC/MS
  • Trip quad MS/MS
  • Sector / quad hybrid MS/MS
Time of Flight
  • Fastest MS analyzer
  • Suited for MALDI
  • High ion transmission
  • MS/MS info from past-source decay
  • Highest practical mass range
  • Requires pulsed ionization method
  • Limited dynamic range
  • Limited precursor-ion selectivity for most MS/MS experiments
  • Very fast GC/MS
Quadrapole Ion Trap
  • High sensitivity
  • Multi-stage mass spec
  • Compact
  • Poor quantitation
  • Poor dynamic range
  • Subject to space charge effects and ion molecule reactions
  • Many parameters define quality of mass spec
  • Benchtop GC/MS, LC/MS and MS/MS
  • Target compound screening
  • Ion chemistry
Ion Cyclotron Resonance
  • High mass resolution
  • Powerful capabilities for ion chemistry and MS/MS experiments
  • Non-destructive ion detection
  • Limited dynamic range
  • Low pressure requirements; therefore need external source for most applications
  • Artifacts present in mass spectra
  • Many parameters define quality of mass spec
  • Ion chemistry
  • High-resolution MALDI and ESI for high mass analytes
  • Laser desorption for materials and surface characterization