Spectra molecular mass from

Observed molecular weights taken from mass spectrum in Figure 7.13c. 

Molecular weight of pyrolysis products directly derivable from mass spectrum through (quasi)molecular ions... 

Multivariate data analysis usually starts with generating a set of spectra and the corresponding chemical structures as a result of a spectrum similarity search in a spectrum database. The peak data are transformed into a set of spectral features and the chemical structures are encoded into molecular descriptors [80]. A spectral feature is a property that can be automatically computed from a mass spectrum. Typical spectral features are the peak intensity at a particular mass/charge value, or logarithmic intensity ratios. The goal of transformation of peak data into spectral features is to obtain descriptors of spectral properties that are more suitable than the original peak list data. 

The amino add analysis of all peptide chains on the resins indicated a ratio of Pro Val 6.6 6.0 (calcd. 6 6). The peptides were then cleaved from the resin with 30% HBr in acetic acid and chromatogra phed on sephadex LH-20 in 0.001 M HCl. 335 mg dodecapeptide was isolated. Hydrolysis followed by quantitative amino acid analysis gave a ratio of Pro Val - 6.0 5.6 (calcd. 6 6). Cycll2ation in DMF with Woodward s reagent K (see scheme below) yielded after purification 138 mg of needles of the desired cyc-lododecapeptide with one equiv of acetic add. The compound yielded a yellow adduct with potassium picrate, and here an analytically more acceptable ratio Pro Val of 1.03 1.00 (calcd. 1 1) was found. The mass spectrum contained a molecular ion peak. No other spectral measurements (lack of ORD, NMR) have been reported. For a thirty-six step synthesis in which each step may cause side-reaaions the characterization of the final product should, of course, be more elaborate. 

During the course of biochemical studies (138). the mass spectrum of 2-acetamidothiazole was recorded its main peaks are the molecular ion (m/e= 142, relative intensity = 26%) and fragments 100 (100), 58 (2. 5), and 43 (39). For 2-acetamido-5-bromothiazole the main peak results again from the loss of C2H2O by the molecular ion. 2-AcetyIacet-amido-4-methylthiazole (2S) exhibits significant loss of from the... 

Mass Spectrometry Ethers like alcohols lose an alkyl radical from their molecular ion to give an oxygen stabilized cation Thus m/z 73 and m/z 87 are both more abun dant than the molecular ion m the mass spectrum of sec butyl ethyl ether... 

Mass Spectrometry Aldehydes and ketones typically give a prominent molecular ion peak m their mass spectra Aldehydes also exhibit an M— 1 peak A major fragmentation pathway for both aldehydes and ketones leads to formation of acyl cations (acylium ions) by cleavage of an alkyl group from the carbonyl The most intense peak m the mass spectrum of diethyl ketone for example is m z 57 corresponding to loss of ethyl radi cal from the molecular ion... 

If the substrate (M) is more basic than NHj, then proton transfer occurs, but if it is less basic, then addition of NH4 occurs. Sometimes the basicity of M is such that both reactions occur, and the mass spectrum contains ions corresponding to both [M + H]+ and [M + NH4]. Sometimes the reagent gas ions can form quasi-molecular ions in which a proton has been removed from, rather than added to, the molecule (M), as shown in Figure 1.5c. In these cases, the quasi-molecular ions have one mass unit less than the true molecular mass. 

The formation of a simple El mass spectrum from a number (p) of molecules (M) interacting with electrons (ep. Peak 1 represents M , the molecular ion, the ion of greatest mass (abundance q). Peaks 2, 3 represent A+, B. two fragment ions (abundances r, s). Peak 2 is also the largest and, therefore, the base peak. 

Electron ionization occurs when an electron beam crosses an ion source (box) and interacts with sample molecules that have been vaporized into the source. Where the electrons and sample molecules interact, ions are formed, representing intact sample molecular ions and also fragments produced from them. These molecular and fragment ions compose the mass spectrum, which is a correlation of ion mass and its abundance. El spectra of tens of thousands of substances have been recorded and form the basis of spectral libraries, available either in book form or stored in computer memory banks. 

In one instrument, ions produced from an atmospheric-pressure ion source can be measured. If these are molecular ions, their relative molecular mass is obtained and often their elemental compositions. Fragment ions can be produced by suitable operation of an APCI inlet to obtain a full mass spectrum for each eluting substrate. The system can be used with the effluent from an LC column or with a solution from a static solution supply. When used with an LC column, any detectors generally used with the LC instrument itself can still be included, as with a UV/visible diode array detector sited in front of the mass spectrometer inlet. 

In a process similar to that described in the previous item, the stored data can be used to identify not just a series of compounds but specific ones. For example, any compound containing a chlorine atom is obvious from its mass spectrum, since natural chlorine occurs as two isotopes, Cl and Cl, in a ratio of. 3 1. Thus its mass spectrum will have two molecular ions separated by two mass units (35 -i- 2 = 37) in an abundance ratio of 3 1. It becomes a trivial exercise for the computer to print out only those scans in which two ions are found separated by two mass units in the abundance ratio of 3 1 (Figure 36.10). This selection of only certain ion masses is called selected ion recording (SIR) or, sometimes, selected ion monitoring (SIM, an unfortunate... 

In a mass spectrum, removal of an electron from a molecule (M) gives a molecular ion (Equation 38.1). The mass of an electron is very small compared with the mass of even the lightest element, and for all practical purposes, the mass of M +is the same as that of M. Therefore, mass measurement of a molecular ion gives the original relative molecular mass of the molecule. 

Typical MS/MS configuration. Ions produced from a source (e.g., dynamic FAB) are analyzed by MS(1). Molecular ions (M or [M + H]+ or [M - H]", etc.) are selected in MS(1) and passed through a collision cell (CC), where they are activated by collision with a neutral gas. The activation causes some of the molecular ions to break up, and the resulting fragment ions provide evidence of the original molecular structure. The spectrum of fragment ions is mass analyzed in the second mass spectrometer, MS(2). 

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

By measuring a mass spectrum of normal ions and then finding the links between ions from the metastable ions, it becomes easier to deduce the molecular structure of the substance that was ionized originally. 

A normal, routine electron ionization mass spectrum represents the m/z values and abundances of molecular and fragment ions derived from one or more substances. 

The mass spectrum of 2-pyrone shows an abundant molecular ion and a very prominent ion due to loss of CO and formation of the furan radical cation. Loss of CO from 4-pyrone, on the other hand, is almost negligible, and the retro-Diels-Alder fragmentation pathway dominates. In alkyl-substituted 2-pyrones loss of CO is followed by loss of a hydrogen atom from the alkyl substituent and ring expansion of the resultant cation to the very stable pyrylium cation. Similar trends are observed with the benzo analogues of the pyrones, although in some cases both modes of fragmentation are observed. Thus, coumarins. 

Molecular ion mass interferences are not as prevalent for the simpler matrices, as is clear from the mass spectrum obtained for the Pechiney 11630 A1 standard sample by electron-gas SNMSd (Figure 4). For metals like high-purity Al, the use of the quadrupole mass spectrometer can be quite satisfiictory. The dopant elements are present in this standard at the level of several tens of ppm and are quite evident in the mass spectrum. While the detection limit on the order of one ppm is comparable to that obtained from optical techniques, the elemental coverage by SNMS is much more comprehensive. 

A SSIMS spectrum, like any other mass spectrum, consists of a series of peaks of dif ferent intensity (i. e. ion current) occurring at certain mass numbers. The masses can be allocated on the basis of atomic or molecular mass-to-charge ratio. Many of the more prominent secondary ions from metal and semiconductor surfaces are singly charged atomic ions, which makes allocation of mass numbers slightly easier. Masses can be identified as arising either from the substrate material itself from deliberately introduced molecular or other species on the surface, or from contaminations and impurities on the surface. Complications in allocation often arise from isotopic effects. Although some elements have only one principal isotope, for many others the natural isotopic abundance can make identification difficult. 

Fullerenes are described in detail in Chapter 2 and therefore only a brief outline of their structure is presented here to provide a comparison with the other forms of carbon. The C o molecule, Buckminsterfullerene, was discovered in the mass spectrum of laser-ablated graphite in 1985 [37] and crystals of C o were fust isolated from soot formed from graphite arc electrodes in 1990 [38]. Although these events are relatively recent, the C o molecule has become one of the most widely-recognised molecular structures in science and in 1996 the codiscoverers Curl, Kroto and Smalley were awarded the Nobel prize for chemistry. Part of the appeal of this molecule lies in its beautiful icosahedral symmetry - a truncated icosahedron, or a molecular soccer ball, Fig. 4A. 

Mass Spectrometry The molecular- ion peak is usually quite small in the mass spectrum of an alcohol. A peak conesponding to loss of water is often evident. Alcohols also fragment readily by a pathway in which the rnoleculai- ion loses an alkyl group from the... 

FIGURE 5.23 Electrospmy mass spectrum of the protein, aerolysin K. The attachment of many protons per protein molecule (from less than 30 to more than 50 here) leads to a series of m/z peaks for this single protein. The inset shows a computer analysis of the data from this series of peaks that generates a single peak at the correct molecular mass of the protein. (Adapted from Figure 2 in Mann, M., and Wilm, M., 1995. Trends in Biochemical Sciences 20 219-224.)... 

No molecular-ion peak is observed in the mass spectrum of isomer 5, although the fragment at m/e 117 [119] is present from loss of the C-l... 

What kinds of information can we get from a mass spectrum Certainly the most obvious information is the molecular weight, which in itself can be invaluable. For example, if we were given samples of hexane (MW = 86), 1-hexene (MW = 84), and 1-hexyne (MW = 82), mass spectrometry would easily distinguish them. 

Both fragmentation modes are apparent in the mass spectrum of 1-butanol (Figure 17.14). The peak at ni/z = 56 is due to loss of water from the molecular ion, and the peak at mjz = 31 is due to an alpha cleavage. 

The mass spectra of all three isomers are different. The ortho isomer loses 17 Daltons (OH, small peak) from its intense molecular ion. The m- and p-isomers lose 16 Daltons from their molecular ions and can be distinguished by comparing the relative abundances of the m/z 65 fragment ion versus their molecular ions. The m/z 65 ion is the most abundant ion in the mass spectrum of the m-isomer (see Figure 22.2), while the molecular ion at m/z 138 is the most abundant ion in the mass spectrum of the p-isomer. 

B. Fragment Ions Common losses from the molecular ions include 90 and 105 Daltons. (See Figure 31.2 for the mass spectrum of the TMS derivative of cholesterol.)... 

---