# Metabolomics/Analytical Methods/Mass Spectrometry/Ion Mobility MS

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## How it works

Ion Mobility Spectrometry (or IMS) is a method in which ions in a gas phase are distinguished/ or separated by the differential migration through a uniform electric field. The first step in IMS is to ionize the molecules. This can be done through a variety of methods including electrospray ionization, using a radioactive source, or corona discharge. Ions are then put into the drift chamber and gating is done by a charged electrode system, although other, more accurate gating mechanisms can also be used. A uniform electric field is then applied in the drift tube once the ions are present which pulls the ions into the drift tube where they encounter the neutral drift molecules in the IMS. The voltage in the tube can have a wide range (a couple volts/cm to hundreds of volts/cm). Ions reach a detector in different orders based on their mobility which is reliant on their mass, shape, and size which can then be graphed based on drift time, resolution and IMS signal in volts. The overall process is very quick, taking only milliseconds.

### IMS machine
## Websites
### Idaho National Laboratory

http://www.inl.gov/index.shtml Idaho National Laboratories (INL) main focus is to find sustainable energy systems and to ensure that energy systems are safe through security. They are currently researching methods to provide more effective and safer nuclear energy. INL also does testing and research to discover and stop national security threats. Ion Mobility is used to test trace explosives and determine there composition. INL is working on creating an IMS with a computerized spectral system to improve the detection restrictions and resolution and simultaneously increase the number of compounds that can be detected. Another improvement they are trying to make with IMS is to make it able to detect differences in money to help stop it from being smuggled. Customs inspectors would be able to use a device to pick up drug traces from the money. IMS is also being combined with global positioning to have chemical mapping that would be able show the precise location of airborne toxins and follow the trail to the source.

#### Terms
##### Leachate

    A product or solution formed by leaching, especially a solution containing contaminants picked up through the leaching of soil.

##### Lignin

    An organic substance that, with cellulose, forms the chief part of woody tissue.

##### Flue

    any duct or passage for air, gas, or the like.

##### Shale

    a rock of fissile or laminated structure formed by the consolidation of clay or argillaceous material.

##### Hemicellulose

    any of a group of gummy polysaccharides, intermediate in complexity between sugar and cellulose, that hydrolyze to monosaccharides more readily than cellulose.

##### Gradiometers

    any instrument used to measure a gradient, as the rate of change of the geomagnetic field.

##### Bitumen

    any of various natural substances, as asphalt, maltha, or gilsonite, consisting mainly of hydrocarbons.

#### Relation to Biochemistry:

IMS is similar to other methods of Mass Spectrometry where the ions have to be ionized first. Like all other MS methods IMS ions are then put into and some kind of field (in IMS electric where some MS methods use a magnetic field). Electrospray Ionization Mass Spec (ESI MS) is a method to prevent breakdown of macromolecular ions while putting them into the gas phase and IMS can also uses electrospray to ionize large molecules so as not to destroy them. IMS can be used to detect and measure the concentration of CO pollutant in air. Since CO has around a 250 fold greater affinity for hemoglobin then oxygen does, a person who breathes in CO suffocates because hemoglobin molecule adsorption sites bound to CO can no longer bind O2 and deliver that to the cells. The high sensitivity of IMS will allow the detection of lower concentrations of CO in the air and allow more time for people to be able to fix the problem or find a place of safety.

### National Institute on Drug Abuse- The Cellular Neurobiology Research Program

http://www.drugabuse.gov/DIR/cell-neuro.html
The Cellular Neurobiology Research Program at the National Institute on Drug Abuse (NIDA) looks at central nervous system (CNS) operation at the cellular level. They focus on neural plasticity, neurodegeneration, neuroanatomical methods, consequences of neurotrophic aspects, electrophysiology, and dopaminergic systems physiological properties. They use MALDI-Ion Mobility time of flight mass spectrometry (MALDI-IM-oTOFMS) to map different compounds present in rat brain tissue. Since cocaine enters the brain where it blocks the reuptake of dopamine, it will be present in the brains of people who use the drug. MALDI-IM-oTOFMS can detect cocaine. In certain disease states, things like lipids and peptides may accumulate, these can also be detected by MALDI-IM-oTOFMS.

#### Terms:
##### Neurotrophic

    relating to the nutrition and maintenance of tissue of the nervous system.

##### Dopaminergic

    Relating to, involved in, or activated by dopamine or related substances.

##### Mesolimbic

    of, relating to, or being the more central portion of the limbic system of the brain that arises mainly in the ventral tegmental area, consists especially of dopaminergic neurons, and innervates the amygdala, nucleus accumbens, and olfactory tubercle the brain's mesolimbic system is involved with the control of memory and emotion.

##### Microiontophoresis

    a process for observing or recording the effect of an ionized substance on nerve cells that involves inserting a double micropipette into the brain close to a nerve cell, injecting an ionized fluid through one barrel of the pipette, and using a concentrated saline solution in the other tube as an electrical conductor to pick up and transmit back to an oscilloscope any change in neural activity.

##### Dynorphin

    any of a group of potent opioids found in the mammalian central nervous system that have a strong affinity for opiate receptors.

##### Chlorisondamine

    A nicotinic antagonist used primarily as a ganglionic blocker in animal research. It has been used as an antihypertensive agent but has been supplanted by more specific drugs in most clinical applications.

#### Relation to Biochemisty:

Metabolic functions are highly controlled in the body because too much of most substances can lead to problems. In an enzyme cascade, if the final product that is needed is not being created, then the pathway will not be inhibited or slowed down at all. When an enzyme is missing or defective in the chain a build up of the substance it is supposed to breakdown/convert will occur. This can lead to disease. Diseases in which lipids build up in the brain include: Niemann-Pick disease, Tay-Sachs Disease, and Fabry’s disease. Niemann-Pick disease is caused by the defective enzyme sphingomyelinase. Because of this defect sphingomyelin cannot be converted to ceramide. This causes a build up of sphingomyelin in the brain which leads to mental retardation and early death. Tay-Sachs disease is caused by the lack of hexosaminidase A and a consequent build up of ganglioside gm2. This also leads to mental retardation and death. Since NIDA also looks at lipid build up in brain tissue, these are some disease they would be able to detect.

### Institute for Analytical Sciences

http://www.isas.de/english/menu-top/research/research-departments/
The Institute for Analytical Sciences (ISAS) is a physical and chemical analysis research center that focuses in biotechnology, spectroscopy, and microfluidics. There five departments work on metabolomics, proteomics, interface spectroscopy, miniaturization, and material analysis. ISAS works to improve current analytical methods. In their study of metabolomics a cell or organisms phenotype or biochemical status is found using quantitative and qualitative analyses. ISAS also uses these analytical methods to understand regulation and cell signaling processes in organisms. They hope to develop analyses that, in one step, will describe a metabolome. Some of ISAS’s current investigations include mold detection and detection of lung cancer through ion mobility spectroscopy.

#### Terms
##### Quadrupole

    a molecule with a quadrupole will have no dipole moment because the two dipoles present in the molecule cancel each other out. A good example is carbon dioxide. A quadropole used in mass spec has four voltage-carrying rods which serve to give ions which travel between them oscillations. Only ions with the right mass/charge ratio (m/z) can undergo these oscillations without hitting one of these rods.

##### Lithography

    A printing process in which the image to be printed is rendered on a flat surface, as on sheet zinc or aluminum, and treated to retain ink while the nonimage areas are treated to repel ink.

##### Plasmon

    The aggregate of cytoplasmic or extranuclear genetic material in an organism.

##### Ellipsometry

    A technique for determining the properties of a material from the polarization characteristics of linearly polarized incident light reflected from its surface.

##### Synchrotron

    an apparatus for imparting very high speeds to charged particles by means of a combination of a high-frequency electric field and a low-frequency magnetic field

##### Geodetic

    The scientific study of the size and shape of the Earth, its field of gravity, and such varying phenomena as the motion of the magnetic poles and the tides.

#### Relation to Biochemistry

ISAS’s work with plants is attempting to better understand how certain essential elements are used at the molecular level including: the mechanisms in which these metals are taken up, placed, and how it is affected by the condition of the plant. As with amino acids, there are elements that organisms must obtain from their diets in order to maintain normal functioning. There are many reactions that occur within cells that require metals. For example, magnesium is used to stabilize the negative charges on the oxygen’s in the phosphate groups in ATP molecules. Magnesium is also required for plant rubisco where it is attached to Lys side chain. Magnesium in this reaction orients the reactants at the active site. Iron is used in many reactions we are already know about and it is possible that there are more places it is used. There are iron-sulfur proteins that take part in redox reactions with one electron where the Fe is reduced or oxidized. ISAS is attempting to find the other ways in which these essential elements are used and acquired.

## Research Articles
### First Detection of Metabolites of the Colon Cancer Cell Line SW 480 Using MCC/IMS and GC/MS

http://ijims.ansci.de/pdf/8/2/Zimmermann_051013.pdf
The Institute for Analytical Sciences in Germany is trying to find biomarkers in colon cancer that could be detected using MCC/IMS and GC/MS in order to find the cancer sooner and increase the survival rate of those who have it. Currently, the methods for detecting colon cancer can be poorly sensitive or invasive. Since cells release certain metabolites and these can be altered when a cell is in a diseased state such as cancer, they are hoping to find metabolites that demonstrate the presence of colon cancer. Since the tests are very rapid there would not need to be much wait time between test and diagnosis. Multi-Capillary-column is used to separate the sample to make sure that compounds separate out properly and then GC/MS is used to specifically identify the metabolites since this cannot be done with IMS alone. The test results found that there were certain ketones and an alcohol that were present in the cancer cells not found in the normal cells. Also, there were peaks in the normal cells for benzaldehyde, methylbenzaldehyde, a different alcohol which are missing from the colon cancer cells.

#### Terms
##### DMEM

    Dulbecco's Modified Eagle's Medium

##### SW 480 cells

    is from a primary (non-metastasized) colon cancer in a patient

##### Aspirate

    To remove (liquids or gases) by means of a suction device.

##### Fetal calf serum

    This is serum taken from embryonic calves. It is used as an important part of media for promoting the growth of tissue cultures. It is not known what causes the tissue cultures to grow, but it probably has to do with growth hormones and other growth factors.

##### Adenocarcinoma

    Cancer that begins in the epithelial cells, which line certain internal organs and have glandular (secretory) properties. Some types of adenocarcinomas include cancers of the breast, thyroid, colon, stomach, pancreas, and prostate, as well as certain types of lung cancer.

##### Solid Phase Microextraction

    a very short gas chromatography column turned inside out. SPME is a fibre coated with an extracting phase, that can be a liquid (polymer) or a solid (sorbent), which extracts different kinds of analytes, from volatile to non-volatile, from different kinds of means, that can be in liquid or gas phase.

#### Relation to Biochemistry

Chromatography can be used to separate many substances. Often it is used in biochemistry to separate proteins based on size, affinity, and charge depending on the different type used. MCC was combined with IMS to increase the amount of information that can be extracted from the sample as in tandem MS when two mass spectrometers are used together (one to separate the peptides and the other to break each peptide to show the amino acid chain). Since cancer cells metabolize so much faster than normal cells, there could be a dramatic decrease in the amount of glucose available to the cells. With the decrease in glucose, the cells might switch to the metabolizing of ketone bodies to maintain energy needs. This could explain the 2 ketone bodies present in the IMS of the cancer cells but not in the normal cells since normally cells would put acetyl-CoA into the citric acid cycle and only small amount of ketone bodies would be formed.

### Ion Mobility Spectroscopy to Detect Lung Cancer and Airways Infections

http://www.spectroscopyeurope.com/MS_18_6.pdf
The research group ISAS is testing IMS techniques to report on ways of diagnosing lung cancer and airway infections early on by detecting minute amounts of volatile metabolites. By combining IMS with a Multi-Capillary Column (MCC) analytes can be detected in less than 600 s with a concentration as low as picograms/liter. ISAS hopes that this device can be used in hospitals to detect different diseases faster and easier. They compared the IMS/MCC samples from people with lung cancer vs. people who were healthy and found 25 variables that distinguish between the two groups that have only a 1.3% error rate. They also found that some bacteria could cause alterations in the IMS of a patient which would help the detection of airway infections.

#### Terms:
##### Beta-radiation

    radiation of beta particles during radioactive decay

##### Sorbent

    a material that sorbs another substance; i.e. that has the capacity or tendency to take it up by either absorption or adsorption

##### Dead Volume

    air that is inhaled by the body in breathing, but does not partake in gas exchange.

##### Faraday Cup

    a metal (conductive) cup designed to catch charged particles in vacuum. The resulting current can be measured and used to determine the number of ions or electrons hitting the cup.

##### Bronchiectasis

    a condition in which an area of the bronchial tubes is permanently and abnormally widened (dilated), with accompanying infection.

##### Serratia marcescens

    the type species of the genus Serratia; a species found in water and soil and milk and foods and insects; can cause infections of the endocardium and blood and wounds and urinary tract and respiratory tract; has been tested as a bioweapon.

##### Haemophilus influenzae

    A gram-negative, rod-shaped bacterium of the genus Haemophilus, especially Haemophilus influenzae type b, that occurs in the human respiratory tract and causes acute respiratory infections, acute conjunctivitis, and purulent meningitis.

#### Relation to Biochemistry:

Cancer cells suck up ATP and therefore have to undergo glycolysis at extremely fast rates. Because of this they end up creating lactate in order to recycle NAD+ to keep up. This build up of lactate could be detected through these IMS methods in lung cancer. Because cancer cells arise from mutations in the genes of a cell and enzymes are often altered or made dysfunctional it is very possible that their products would build up which could then be detected using something like the IMS/MCC technique. Since people who have diabetes get a build up of acetone which is released in the breath, this is another compound that can be detected using this analytical method. In people with diabetes the liver incompletely oxidizes fatty acids in high amounts. Acetyl-CoA cannot be oxidized by the Citric Acid Cycle and builds up. Some acetyl-CoA is then converted to acetoacetate which is then decarboxylized spontaneously to form acetone. Acetone is then exhaled in the breath.

### Development of high throughput dispersive LC-ionmobility-TOFMS techniques for analysing the human plasma proteome

http://bfgp.oxfordjournals.org/cgi/reprint/3/2/177
The researchers have developed a technique that combines IMS with mass spectrometry, collision-induced dissociation (CID), and reversed-phase liquid chromatography. The combination of these methods is used to take the enzymatic breakdown of protein mixtures and analyze the peptides that result. Liquid chromatography first separates the peptides which are then subjected to electrospray ionization which puts them into a gas phase. These ionized peptides are then separated in the gas phase by the IMS. CID is then used to break up the peptides where they are then placed into an MS to determine the mass of each analyte. The human plasma proteome was picked to be tested because there are many proteins in plasma that have not been discovered yet.

#### Terms
##### Reversed phase chromatography

    includes any chromatographic method that uses a non-polar stationary phase.

##### RF-focusing device

    element that ionizes the electrons by emitting a radio frequency signal

##### Paul geometry traps

    A type of liner quadropole ion trap that uses DC and radio frequency oscillating AC electric fields to trap ions

##### Uromodulin

    a substance produced by cells of the ascending limb of the loop of Henle; it is a normal constituent of urine and is the major protein constituent of urinary casts.

##### Lyophilized

    To freeze-dry (blood plasma or other biological substances).

#### Relation to Biochemistry

Electrospray ionization is used to make sure that the macromolecules are not destroyed in the process of switching them to the gas phase. In electrospray ionization, the sample is passed through a charged, high electrical potential. The needle scatters the sample as tiny charged droplets. The non-destructed charged macromolecular ions are left when the solvent around them evaporates rapidly. The paper talks about how certain low-amount proteins such as those from post-translational modifications and membrane proteins would be difficult to detect although they would be of high interest. Posttranslational modification includes enzymatic processing where phosphorylation, removal of amino acids, carboxylation, or addition of prosthetic groups. Posttranslational modifications are important for maintaining control within the cell. If proteins were always active then many metabolic functions would occur uncontrollably, so only small amounts of a protein at a time would be in an active state.

## Wiki-d Links

http://en.wikipedia.org/wiki/Ion_mobility_spectrometry http://en.wikipedia.org/wiki/DART_ion_source http://en.wikipedia.org/wiki/Bradbury-Nielsen_shutter http://en.wikipedia.org/wiki/Electron_mobility http://en.wikipedia.org/wiki/Mass_spectrometry

## Articles and Web Pages for Review and Inclusion

Peer-Reviewed Article #1:
Monitoring Dynamic Changes in Lymph Metabolome of Fasting and Fed Rats by Electrospray Ionization-Ion Mobility Mass Spectrometry (ESI-IMMS)
Anal. Chem., 2009, 81 (19), pp 7944–7953'"

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       Identify the main focus of the resource. Possible answers include specific organisms, database design, intergration of information, but there are many more possibilities as well.

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#### Summary

       Enter your article summary here. Please note that the punctuation is critical at the start (and sometimes at the end) of each entry. It should be 300-500 words. What are the main points of the article? What questions were they trying to answer? Did they find a clear answer? If so, what was it? If not, what did they find or what ideas are in tension in their findings?

#### Relevance to a Traditional Metabolism Course

       Enter a 100-150 word description of how the material in this article connects to a traditional metabolism course. Does the article relate to particular pathways (e.g., glycolysis, the citric acid cycle, steroid synthesis, etc.) or to regulatory mechanisms, energetics, location, integration of pathways? Does it talk about new analytical approaches or ideas? Does the article show connections to the human genome project (or other genome projects)?