Glossary

also called Collisionally-Activated Decomposition, or CAD, CID is the most common method of fragmentation of a precursor ion into product (or fragment) ions; this fragmentation process occurs within a collision cell (or, alternatively, within a trap) containing an energized, chemically-inert collision gas (e.g., Ar, He, N2, CO2, etc.) at high pressure; for more, see http://www.chm.bris.ac.uk/ms/theory/cid-fragmentation.html
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a form of liquid chromatography that is used to separate or purify proteins from complex mixtures; columns used for FPLC can separate proteins based on properties such as size, charge distribution, hydrophobicity, or affinity
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also called Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, or FT-ICR MS, FTMS uses ion cyclotron resonance to select and detect ions; this method takes advantage of the fact that ions have a fundamental oscillation frequency in a magnetic field; for more, see http://www.bumc.bu.edu/ftms/modern-instrumental-biochemistry/ftms-introduction/
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HPLC is a form of column chromatography in which the solvent is forced through the column under high pressures of up to 400 atmospheres, making the chromatography procedure much faster; because HPLC allows one to use a much smaller particle size for the column packing material (resulting in a much greater surface area for interactions between the stationary phase and the molecules flowing past it), an improved separation of the components of the mixture can be achieved; for more, see http://www.chemguide.co.uk/analysis/chromatography/hplc.html
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a high resolution ion isolation method that achieves improved selectivity and isolation efficiency of labile ions; because HRI separates precursor ions with high resolution, mass spec analysis can be performed without interference from isotopic ions; for more, see http://www.thermo.com/com/cda/resources/resources_detail/1,,112802,00.html?fromPage=search
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a quantitative proteome analysis method that uses post-isolation stable isotope labeling of proteins with a class of reagents termed isotope-coded affinity tags (ICAT); the ICAT method enables accurate measurements of small changes in relative protein levels; for more, see Gygi SP, et al., NATURE BIOTECHNOLOGY vol 17 October 1999 @ http://biotech.nature.com
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also known as electrofocusing, IEF is an electrophoretic method in which proteins are separated on the basis of their isoelectric points (pI’s), thus allowing separation of proteins that differ by as little as a single charge
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a mass spec-based approach for the relative quantification of proteins; this approach utilizes iTRAQ™ reagents (reagents that covalently derivatize primary amino groups and lysine side chains at the N-terminus of peptides by introducing stable isotopes)
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a soft ionization mass spectrometry technique where by ionization of biomolecules is triggered by a laser beam and the resulting ions are formed directly from the solid (matrix-embedded) state; a matrix is used to prevent the destruction of biomolecules by the laser beam and to facilitate vaporization and ionization; for more, see Andersen JS, et al., NATURE BIOTECHNOLOGY vol 14 April 1996 @ http://www.nature.com/naturebiotechnology
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a method that couples 2D-LC to MS/MS in order to resolve and identify peptides from complex mixtures; this method utilizes a microcolumn that is packed with two independent chromatography phases (a strong cation exchanger and a reversed-phase matrix material) to separate peptides which, as they elute from the column, are then directed to the ESI ion-trap mass spectrometer; for more, see http://cshprotocols.cshlp.org/cgi/content/full/2006/28/pdb.prot4555
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a triple-quadrupole mass spectrometer in which the third quadrupole is replaced with a time-of-flight (TOF) mass spectrometer; in a Q-TOF mass spectrometer, the first quadrupole selects the parent molecule for analysis, the second quadrupole fragments the parent molecule, and then the time-of-flight mass spectrometer provides a mass analysis of the fragment ions
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a chromatography technique in which the mobile phase is a liquid
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a technique that combines liquid chromatography (LC) (for physical separation of the components of a mixture) with mass spectrometry (MS) (for mass analysis of the components); the physical interface between the LC technique (which involves liquid) and the MS technique (which involves gas) is most often an electrospray or nanospray ion source
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a technique that combines liquid chromatography (LC) (for physical separation of the components of a mixture) with tandem mass spectrometry (MS/MS) (for mass-based selection and analysis of the components); tandem mass spectrometry (MS/MS) involves multiple rounds of mass spectrometry where during the first stage of mass spectrometry a precursor (parent) ion is selected based on mass, the selected ion is then fragmented (e.g., in a collision cell) into product ions, and the resulting product ions are then separated based on mass by a second stage of mass spectrometry
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an instrument that measures the masses of indiviual molecules that have been converted into ions; a mass spectrometer does not actually measure the molecular mass directly, but rather the mass-to-charge ratio (m/z) of the ions formed from the molecules and then the mass spec system converts this information into a mass spectrum; for more, see http://www.asms.org/whatisms/qindex.html
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a technique in which the mass spectrometer is set to scan over a very small specific mass range, typically one mass unit; only ions with a mass within this narrow mass range are detected and plotted; a SIM plot usually does not lead to a unique identifier for the analyzed molecule because a SIM plot of a very complicated sample (e.g., serum or plasma) will contain a number of peaks due to the fact that many different ions have the same m/z value; however, a SIM experiment is more sensitive than a full scan experiment; for more, see http://www.ionsource.com/tutorial/msquan/intro.htm
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a technique for performing mass spectrometric quantitation of a specific unique fragment ion within a very complicated matrix; in an SRM experiment, a parent ion is selected for fragmentation based on its mass and then, once the fragment (product) ions are formed, a single fragment ion is specifically monitored; SRM plots are very simple, usually containing only a single peak; for more, see http://www.ionsource.com/tutorial/msquan/intro.htm
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a protein-labeling method, used for mass spec-based comparative proteomic studies, that involves metabolic (in vivo) incorporation of stable-isotope-labeled amino acids into proteins; in a SILAC experiment, two cell populations are grown in culture media that are identical except that one of them contains a 'light' and the other a 'heavy' form of a particular amino acid; the resulting 'light' and 'heavy' proteomes can then be distinguished by mass spec analysis without having to perform any chemical derivatization or protein purification; for more, see http://www.silac.org/
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the use of multiple SRM analyses to monitor two or more specific fragment (product) ions that have been generated from a single parent ion
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the weight of a molecule equaling the sum of the weights (expressed in daltons) of the atoms of which the molecule is made
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polyacrylamide gel electrophoresis (PAGE) in the presence of the anionic detergent sodium dodecyl sulfate (SDS); SDS dissociates proteins into their constituent polypeptide chains which are then separated during SDS-PAGE according to their molecular weight; thus the molecular weight of the polypeptide chains of a given protein can be determined by comparing their electrophoretic mobility on SDS gels to the mobility of polypeptide chains of known molecular weights; for more, see http://www.xtal-protocols.de/prot/sds.html
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a method for quantitation of peptides in complex mixtures; this method utilizes anti-peptide antibodies that are immobilized on a nanoaffinity column in order to enrich specific peptides along with spiked stable-isotope-labeled internal standards of the same sequence; upon elution from this nanoaffinity column, the peptides (natural and labeled) are quantitated by electrospray mass spectrometry; for more, see Anderson NL, et al., Journal of Proteome Research, 2004, 3 (2), pp 235-244
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a version of HPLC in which peptides are separated based on their hydrophobic character; this is achieved by virtue of the fact that peptides bind to reverse phase (RP) HPLC columns when in a high aqueous environment (high aqueous mobile phase) and elute from RP HPLC columns when the mobile phase is switched to a high organic solvent; peptides are separated from each other by running a linear gradient of the organic solvent; for more, see http://www.ionsource.com/tutorial/chromatography/rphplc.htm
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in contrast to 'normal' phase chromatography, where the adsorbent surface is hydrophilic and, thus, has a stronger affinity for polar compounds, 'reverse' phase chromatography uses a non-polar stationary phase with a liquid mobile phase composed of water combined with an organic solvent, resulting in a 'reversed' elution order of the molecules that are being separated; i.e., polar molecules are eluted first while non-polar molecules are retained
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a form of ion-exchange chromatography in which molecules in a mixture are separated based on their total charge
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an ion that undergoes fragmentation to form product ions
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an ion that results from fragmentation of a precursor ion; also referred to as a fragment ion
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from Thermo Fisher Scientific Inc, the LTQ Orbitrap XL™ hybrid FTMS (Fourier Transform Mass Spectrometer) is based on the LTQ XL™ linear ion trap and Orbitrap™ technology, resulting in an instrument with a rapid scan rate, high mass accuracy, and up to 100-K resolution power; for more, see http://www.thermo.com/com/cda/product/detail/1,,10131071,00.html
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