Glossary

• Amino Acid: The building block of a protein. In the process of translation, an RNA sequence is translated into a protein sequence, one amino acid at a time. Amino acids have an amino (NH3) terminal (called the N-terminal) and a carboxyl (CO2) terminal (called the C-terminal). When a peptide grows in translation, the C-terminal of the next amino acid is covalently bonded to the N-terminal of the last amino acid. There are 20 amino acids in the standard amino acid alphabet.
• Atmospheric Pressure Chemical Ionization (APCI): An ionization method using heat and electrical current to ionize small molecules. Compare to ElectroSpray Ionization (ESI).
• Atmospeheric Pressure Photo Ionization (APPI): An ionization method similar to APCI that uses light instead of electrical current.
• Avogadro's number: The number of molecules in one mole of the given molecule, 6.02x10^23
• Charge envelope: The pattern of spectra produced by the ionization of a larger molecule. Multiple peaks at different values of mass-to-charge will be present for a charge envelope, corresponding to different charge states for the molecule of interest.
• Collision cell: A component of a tandem or ms^n mass spectrometer. The collision cell occurs between successive measurements of the mass-to-charge ratio, and utilizes a method of breaking chemical bonds within a selected molecule to create daughter ions from the parent species.
• Collision gas: A gas, usually inert or noble, that can be used in tandem mass spectrometry to induce fragmentation of parent ion into daughter ions. Noble gases are prefered for this application because while they can induce fragmentation under pressure, they ordinarily will not form covalent bonds with the daughter ions.
• Dalton: A unit of molecular mass. One hydrogen ion (or one proton) weighs one Dalton
• Daughter Ions: Daughter ions are created in tandem or ms^n mass spectrometry. These are ions of a lower mass than the selected parent ion - though due to distribution of charge, the daughter ions may have a lower or higher mass-to-charge ratio.
• Deconvolution: The process of solving the accurate mass of a large molecule from its charge envelope. This process is required for solving mass anytime an ionization method is used that applies variable charge to a population of molecules (such as electrospray ionization).
• Electrospray Ionization (ESI): An ionization method developed by JB Fenn for mass spectrometry. Specifically aids in ionization of a liquid mixture to the gas phase for mass spectral analysis
• Fragmentation: A process of dividing a parent ion into component daughter ions. This is often done through the use of a collision gas, though other methods exist as well.
• Genome: The full DNA sequence of an organism.
• Genomics: The study of the genome of an organism.
• Hexapole: Six parallel metal rods, precisely arranged to allow selection and/or obsevation of ions as they pass through a mass spectrometer. Similarly to a quadrupole, a hexapole may be controlled by RF, DC, or both, depending on the application. Hexapoles are frequently used for filters or collision cells.
• Hydrophobicity: Literally, "water fearing", hydrophic molecules do not dissolve readily (if at all) in water. Various factors contribute to make a molecule hydrophic, and this trait is commonly used to separate molecules in Liquid Chromatography.
• Interactomics: The study of interactions within a cell. This can include protein-protein, protein-nucleic acid, protein-environment, and other interactions.
• Ion: A charged molecule. Common ions in biology include Sodium and Chloride. The charged nature of ions is used in measuring the mass-to-charge ratio of ions in mass spectrometry.
• Isotope: An atom with an atomic weight different than the prevailing species of the same atom. Carbon-13 is an isotope of Carbon, which is much more abundant as Carbon-12. Isotopes in nature can be observed in mass spectrometry analysis of molecules.
• ICAT: Isotope-Coded Affinity Tagging. A method taking advantage of mass shifts from isotopes to observe differential expression of proteins. This is a common proteomics method.
• Liquid Chromatography (LC): A chemical technique that can be used to separate a mixture of molecules in solution. Depending on the chemistry used in the LC application, molecules can be sorted by any of a number of chemical or physical traits.
• MALDI: Matrix Assisted Laser Desorption/Ionization. An ionization method developed by Shimadzu Corporation that utilizes a chemical matrix to ionize molecules with a laser.
• Multi Channel Plate (MCP): A mass detector used in many mass spectrometers. The MCP is generally configured to determine the mass-to-charge ratio of ions based on the time information of a Time Of Flight (TOF) tube.
• Orbitrap: A relatively new style of mass detector, developed by Alexander Makarov. The orbitrap studies the waveform of an ion, similar to an ion cyclotron; though in much smaller physical space. The technology for the orbitrap is currently owned by Thermo.
• Parent Ions: Parent ions are observed in mass spectrometry, and are primarily of importance in tandem or ms^n mass spectrometry. A parent ion is a species of interest for molecular analysis through the use of a collision cell, through which are created daughter ions.
• Proteome: The collection of all proteins in a cell, organ, or species. In comparison to a genome, a proteome is more dynamic. For example, while the genome of a kidney cell is the same as a cardiac cell (within the same species), the proteomes of the two cell types are different. Similarly some cell types have distinctly different proteomes at different times or in response to different conditions.
• Proteomics: The study of a proteome.
• Quadrupole: Four metal rods running in parallel, generally arranged so as to have a central route through the middle of them for ions to flow through. The arrangement is similar to the points on a compass. Depending on the installation, quadrupoles are controlled by radio frequency (RF), direct current (DC), or both. The charge of the quadrupole rods can allow for both the measurement and selection of ions by their mass-to-charge ratio.
• Q-TOF: An instrument that uses both a Quadrupole and a Time Of Flight (TOF) for measurement of ions in tandem mass spectrometry. Generally the Quadrupole is used as a mass filter, with either another quadrupole or a hexapole used for a collision cell, followed by a TOF for monitoring the daughter ions. Q-TOF and Triple Quadrupole instruments are used similarly but differ in their construction.
• SELDI: Surface Enhanced Laser Desorption/Ionization. An ionization method similar to MALDI that uses surface-based chemistry rather than a chemical matrix on an inert surface.
• Shooting: Shooting is a slang term used in mass spectrometry that refers to the act of ionizing samples for mass spec. Shooting can refer to the action of the laser in MALDI/SELDI, or the act of atmospheric pressure (such as ESI) ionization from liquid phase. However, the term "shooting" can have unfortunate connotations when investigating pharmaceutical compounds - for example "shooting morphine", which certainly legal to do on a mass spec, could evoke the wrong idea in an unfamiliar crowd.
• Tandem Mass Spectrometry: A mass spectrometry method that involves selecting an ion population (generally by its mass-to-charge ratio) and then using a collision cell to produce daughter ions. This is often used in the process of peptide sequencing.
• Time Of Flight (TOF): A method for determining the mass-to-charge ratio of an ion based on the time it takes for the ion to travel a known distance under vacuum. TOF is generally done in a tube-like apparatus, hence the term "TOF tube".
• Time to Digital Converter : The output from a TOF detector is a time-based signal - which is generally analog in nature - needs to be converted to a digital signal for computational analysis and interpretation. The TDC is responsible for handling the timing and gating of molecules for TOF.
• Triple Quadrupole: An instrument that uses three quadrupoles to do tandem mass spectrometry. The general setup for this is the first quadrupole (Q1) is a mass filter, the second quadrupole (Q2) is a collision cell, and the third quadrupole (Q3) measure the daughter ions. A triple quad and a Q-TOF are functionally similar though their methods differ. Triple Quadrupole instruments are referred to casually as "triple quads".
• Trypsin: A biological enzyme that cleaves proteins into smaller peptides. In particular, trypsin cleaves after the amino acids lysine or arginine (provided they are not followed by proline), which will generally cleave a complete protein into a number of peptides.