Ion structural information

It is possible to derive structural information from the fragmentation pattern in a spectrum. The appearance of prominent peaks at certain mass numbers is empirically correlated with certain structural features. For example, the mass spectrum of an aromatic compound is usually dominated by a peak at m/z 91, corresponding to the tropylium ion. Structural information can also be obtained from the differences between the masses of two peaks in a spectrum. For instance, a fragment ion occurring 20 mass numbers below the molecular ion strongly suggests a loss of a HF moiety. Thus, a fluorine atom is likely to be present in the substance analyzed. 

Because of these powerful qualitative capabilities, FTICR mass spectrometry is especially useful for characterization of DCLs. Because the composition of the DCL cannot be statically defined, except when in equilibrium with the receptor, it is essential to be able to identify the components at this stage. Using FTICR MS, identification can be done by a combination of exact mass determination and tandem-in-time mass spectrometry to yield par-ent/daughter ion structural information. Although FTICR is an expensive option for combinatorial library characterization, it can provide the most direct information for ligand identification in libraries. 

Mass spectra have been used principally for the determination of molecular weights and deduction of the detailed composition of the molecule from the isotopic patterns of the various ions. Structural information can also be obtained from a detailed analysis of the fragmentation pattern. The clusters which have been studied by mass spectrometric methods have largely been carbonyl, 7r-cyclopentadienyl, and carbonyl hydride clusters, and references to these studies have been included in Tables II, VIII, and III, respectively. 

Structurally, glycosphingolipids and gangliosides are distinct from other classes of lipids they are made of a hydrophobic ceramide lipid tail to which an oligosaccharide head group is attached. Characterization of glycosphingolipids and gangliosides is achieved by CID-MS/MS of the FAB-, ESI-, and MALDI-produced [M - - H]+ and [M — H] ions. Structural information on ceramide and carbohydrate portions can be also derived. 

While the inherent trapping capability provides enhanced sensitivity, and the tandem-in-time mode of operation provides enhanced ion structure informing power (MS ) relative to linear Q-based instruments, these same features also lead to decreased quantitative performance of 3D traps compared to QqQs in MRM mode. This is largely due to the fact that the total scan times associated with full scan MS/MS on a trap are inherently longer than those required for MRM on a QqQ-In addition, unlike a QqQ that provides constant scan times over the elution of the chromatographic peak, scan times on an ion trap vary due to the need to control the population of ions stored in the trap to avoid the decreased performance (resolution and sensitivity) that comes with space charge effects. These variations in scan times leads to poorer precision of chromatographic peak areas across replicate injections. Further, should a stable isotope labeled SIS be used in the analysis, the 3D... 

Steroid sulfates and glucuronides are best analyzed in the negative-ion ESI mode, where they give [M-H] ions. Structural information can then be obtained by performing MS/MS (Figure 14.5). However, steroids and bile acids exist in biological samples as part of complex mixtures and an [M-H] ion is likely to represent a number of isomers. These can, however, be separated by LC prior to ESI [27] and partially characterized by MS/MS [34]. 

In contrast to IR and NMR spectroscopy, the principle of mass spectrometry (MS) is based on decomposition and reactions of organic molecules on theii way from the ion source to the detector. Consequently, structure-MS correlation is basically a matter of relating reactions to the signals in a mass spectrum. The chemical structure information contained in mass spectra is difficult to extract because of the complicated relationships between MS data and chemical structures. The aim of spectra evaluation can be either the identification of a compound or the interpretation of spectral data in order to elucidate the chemical structure [78-80],... 

Because there is little fragmentation on FD, it is necessary to activate the molecular or quasi-molecular ions if molecular structural information is needed. This can be done by any of the methods used in tandem MS as, for example, collisional activation (see Chapters 20 through 23 for more information on tandem MS and collisional activation). 

Ions formed in an electrospray or similar ion source are said to be thermolized, which is to say that their distribution of internal energies is close to that expected for their normal room-temperature ground state. Such ions have little or no excess of internal energy and exhibit no tendency to fragment. This characteristic is an enormous advantage for obtaining molecular mass information from the stable molecular ions, although there is a lack of structural information. 

A single instrument — a hybrid of a quadrupole and a TOF analyzer — can measure a full mass spectrum of ions produced in an ion source. If these are molecular ions, their relative molecular mass is obtained. Alternatively, precursor ions can be selected for MS/MS to give a fragment-ion spectrum characteristic of the precursor ions chosen, which gives structural information about the original molecule. 

Prior separation of mixtures into individual components may not be needed. If the mass spectrometer is capable of MS/MS operation, one of the mass spectrometers is used to isolate individual ions according to m/z value (mass-to-charge ratio), and the other is used to examine their fragmentation products to obtain structural information. 

The previous discussion has centered on how to obtain as much molecular mass and chemical structure information as possible from a given sample. However, there are many uses of mass spectrometry where precise isotope ratios are needed and total molecular mass information is unimportant. For accurate measurement of isotope ratio, the sample can be vaporized and then directed into a plasma torch. The sample can be a gas or a solution that is vaporized to form an aerosol, or it can be a solid that is vaporized to an aerosol by laser ablation. Whatever method is used to vaporize the sample, it is then swept into the flame of a plasma torch. Operating at temperatures of about 5000 K and containing large numbers of gas ions and electrons, the plasma completely fragments all substances into ionized atoms within a few milliseconds. The ionized atoms are then passed into a mass analyzer for measurement of their atomic mass and abundance of isotopes. Even intractable substances such as glass, ceramics, rock, and bone can be examined directly by this technique. 

Ionization Method Type of Molecular Ion Formed Good Molecular Mass Information Abundant Fragment Ions MS/MS Needed for Structural Information Accurate Values for Isotope Ratios... 

Since detailed chemical structure information is not usually required from isotope ratio measurements, it is possible to vaporize samples by simply pyrolyzing them. For this purpose, the sample can be placed on a tungsten, rhenium, or platinum wire and heated strongly in vacuum by passing an electric current through the wire. This is thermal or surface ionization (TI). Alternatively, a small electric furnace can be used when removal of solvent from a dilute solution is desirable before vaporization of residual solute. Again, a wide variety of mass analyzers can be used to measure m/z values of atomic ions and their relative abundances. 

Additional ionization occurs by collision between the ions and other neutral species (ion/molecule collision see Chapter 1). Unless special steps are taken (see Chapters 8 and 11 ), the ions formed do not fragment, so little or no structural information is obtained. However, the lack of fragmentation does mean that good relative molecular mass data can be obtained. The assembly of ions formed by ion... 

The last three detection schemes apply only under very special circumstances. Transmission EXAFS is strictly a probe of bulk structure, i.e., more than about a thousand monolayers. The electron- and ion-yield detection methods, which are used in reflection rather than transmission schemes, provide surface sensitivity, 1-1,000 A, and are inherendy insensitive to bulk structure. X-ray fluorescence EXAFS has the widest range of sensitivity—from monolayer to bulk levels. The combination of electron or ion yield and transmission EXAFS measurements can provide structural information about the X-ray absorbing element at the surface and in the bulk, respectively, of a sample. 

Tandem mass spectrometry (MS/MS) is a method for obtaining sequence and structural information by measurement of the mass-to-charge ratios of ionized molecules before and after dissociation reactions within a mass spectrometer which consists essentially of two mass spectrometers in tandem. In the first step, precursor ions are selected for further fragmentation by energy impact and interaction with a collision gas. The generated product ions can be analyzed by a second scan step. MS/MS measurements of peptides can be performed using electrospray or matrix-assisted laser desorption/ionization in combination with triple quadruple, ion trap, quadrupole-TOF (time-of-flight), TOF-TOF or ion cyclotron resonance MS. Tandem... 

Neutral Loss Only a limited number of neutral fragments of low mass which are eliminated in decompositions of molecular ions. Examples are H, H2, CH3 and OH. Therefore, the presence of a major ion below the molecular ion at an improbable interval (eg, loss of 4 to 14, 21 to 25 amu) will indicate that the latter is not the molecular ion Postulation of Molecular Structures The. postulation of the structure of an unknown molecule is based on several major kinds of general structural information available in the mass spectmm. McLafferty (Ref 63) suggests the following systematic approach ... 

The packing arrangement of cation and anion in diazonium salts has important implications not only for the structure of diazonium ions, as discussed above, but also for the solid-state chemistry of these compounds, in particular with regard to halogeno-de-diazoniations such as the Schiemann reaction. TWo of the papers of Gougoutas (1978, with Johnson, and 1979) contain, in addition to the X-ray analyses, experimental results on bromo- and iodo-de-diazoniation, which can be interpreted on the basis of the structural information (see Secs. 10.4-10.6). 

The ion spray liquid chromatography/mass spectrometry (LC-MS) interface coupled via a postsuppressor split with an ion chromatography (IC) has been used in the analysis of alcohol sulfates. The IC-MS readily produces the molecular weight while the tandem mass spectrometric detection IC-MS-MS provides structural information [305]. 

Further structural information is available from physical methods of surface analysis such as scanning electron microscopy (SEM), X-ray photoelectron or Auger electron spectroscopy (XPS), or secondary-ion mass spectrometry (SIMS), and transmission or reflectance IR and UV/VIS spectroscopy. The application of both electroanalytical and surface spectroscopic methods has been thoroughly reviewed and appropriate methods are given in most of the references of this chapter. 

Mass spectrometry (see Chapter 3) is capable of providing molecular weight and structural information from picogram amounts of material and to provide selectivity by allowing the monitoring of ions or ion decompositions characteristic of a single analyte of interest. These are the ideal characteristics of both a qualitative and a quantitative detector. 

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