Analyzing the Fragments

The majority of the peaks in a mass spectrum are produced from fragmentation of the molecular ion. In this section, we will explore the characteristic fragmentation patterns for a number of compounds. These patterns are often helpful in identifying certain structural features of a compound, but it is generally not possible to use the fragmentation patterns to determine the entire structure of the compound. 

The various carbocations that can result from the fragmentation of pentane. 

Icosane is a straight-chain hydrocarbon consisting of 20 carbon atoms connected by 19 C—C bonds. Each of these bonds is susceptible to fragmentation to produce a cation that is detected by the mass spectrometer. Each one of these 19 possible carbocations appears in the spectrum as a group of peaks (except for the M—15 peak, which has a very small relative abundance). 

When analyzing a fragment peak, the key is to look at its proximity to the molecular ion peak. For example, a signal at M—15 indicates the loss of a methyl group, and a signal at M-29 indicates the loss of an ethyl group. The likelihood of fragmentation increases with the stabihty of the carbocation formed as well as the stability of the radical that is ejected. 

As another example, consider the most likely fragmentation of the following molecular ion. 

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Triple quadrupole In the standard configuration, the first quadrupole is used to select a specific ion mass, the second quadrupole is a collision cell that induces the selected ion mass to fragment, and the third quadrupole is used to analyze the fragments. The triple quadrupole is a very popular choice for very sensitive and quantitative analysis of complex mixtures (e.g., drug analysis). 

According to Section 4.1.1 the wavepacket is a superposition of stationary wavefunctions corresponding to a relatively wide range of energies. This and the superposition of three apparently different types of internal vibrations additionally obscures details of the underlying molecular motion that causes the recurrences. A particularly clear picture emerges, however, if we analyze the fragmentation dynamics in terms of classical trajectories. 

LC-MS is a quick and accurate analytical tool for determining the composition of 99mTc radiopharmaceuticals. It also supplements structural information obtained from other analytical methods such as NMR. Therefore, LC-MS may also be a complimentary technique for structure determination of radio-labeled compounds by analyzing the fragmentation patterns of the mass spectra. LC-MS has the potential to become a routine analytical tool for radiopharmaceuticals labeled with 99mTc or other radioisotopes such as 186Re. 

Eventually, fragment the selected ions and analyze the fragments in a second analyser. 

The sum of the 2d. and 3d. enrichments were measured by monitoring the ratio of Ihe ion Sundance at m/e 116.1 to that at m/e 115 1 in the El spectrum. The ionic fragment at mass 115 1 contains both the 2 and 3 carbon of glucose. However, it does not contain the number 6 carbon. This was verified by analyzing the fragmentation patterns of the three infusates individually. 

Tandem mass spectrometers are either triple quadrupole systems (the collision cell is also a quadrupole) or quadrupole ion-trap spectrometers. A triple quadrupole mass spectrometry system is shown in Figure 32F-2. Here, the first quadrupole acts as a mass filter to select the ion of interest. This ion is then fragmented by collision with an inert gas in the collision cell. The final quadrupole mass analyzes the fragments produced. The triple quadrupole system can be operated in other modes. For example, if the first quadrupole is operated as a wide mass filter to transmit a wide range of ions and no collision gas is present in the collision cell, the instrument is operating as an LC/MS system. The instrument can be operated by scanning one or both quadrupoles to produce mass spectra of the fragments of ions selected by the first quadrupole as that quadrupole is scanned. 

We may formulate the products by substituting hydroxyl groups for each cleaved bond and analyzing the fragments. 

If we had an instrument with three mass analyzers, the fragmentation process could be repeated before final analysis. A precursor ion is selected, fragmented, a given product ion is selected and fragmented again before mass analysis of its product ions that is ... 

Methods have also been developed to evaluate the average MWs by analyzing the fragments produced with SIMS from the surfaces of polymer materials. Studies conducted by Galuska on a variety of hydrocarbon elastomers (polyisoprene [PIP], polybutadiene [PBD], and PIB) and thermoplastics (polyethylene [PE], PS, polypropylene [PP], and poly(1-butene) [Pl-B]) [133] demonstrated that the relative intensity of the protonated monomer (F) can be correlated with the average MWs (M ), according to the general relationship ... 

This type of scan is often used to analyze the fragmentation pattern of a substance. The spectra obtained may serve as a finger print of an ion and may allow a fragmentation scheme to be established. For a known reaction of a known compound the instrument can be set to detect only this one signal on this particular B/E=const, surface, enhancing the specificity of detection (see reaction monitoring. Chap. 20.2). 

MS spectra with fragmentation of molecules require collision-activated dissociation (CAD) and triple quadrupole analyzers. In these instruments, the analysis is performed as follows the first quadrupole selects the interesting ion (parent ion), the second produces the fragments from the isolated ion, and the third quadrupole analyzes the fragmentation products (daughter ion spectmm). These steps (ion isolation, fragmentation, and analysis) can be repeated by addition of n quadrupole devices (multisector mass spectrometer) to allow multiple MS/MS experiments (MS") to be performed. 

In this section, we will use EI-MS data to determine the structure of two unknown compounds. Even if the compound you are analyzing is not in searchable MS databases available to you, it is still possible to determine the structure of the compound with a few key pieces of data. If the molecular formula is available, either from an exact mass determination (Section 3.6) or Rule of Thirteen analysis (Section 1.5) on the molecular ion, the process is much simpler. Furthermore, knowing the main functional group(s) in the compound will assist in analyzing the fragmentation pattern. Information from an infrared spectrum and/or NMR spectra are useful in this regard. 

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