Fulton G. Kitson

Chapter 1 – What Is GC/MS?

This chapter provides a brief introduction to gas chromatography/mass spectrometry (GC/MS). The operating principle of a gas chromatograph includes volatilization of the sample in a heated inlet port, separation of the components of the mixture in a prepared column, and detection of each component by a detector. Carrier gases such as hydrogen or helium are important elements of the gas chromatograph. It is used to transfer the sample from the injector through the column, and into the detector. The interface in GC/MS is a device for transporting the effluent from the gas chromatograph to the mass spectrometer. The most common mass spectrometers interfaced to gas chromatographs are called “quadrupole” and “magnetic-sector instruments.” The detection of ions in GC/MS is performed exclusively using an electron multiplier. There are two types of electron multipliers: the continuous dynode type and the discrete type. The chapter discusses various ionization methods such as electron impact ionization, chemical ionization, and negative ion chemical ionization.

Chapter 9 – Amino Acids

This chapter focuses on gas chromatography (GC) separation and derivatization of amino acids (AAs) and PTH-amino acids. The TBDMS derivatives are stable for at least one week. If the reaction time for the TBDMS derivatives is not long enough, a mixture of mono- and di-TBDMS derivatives is observed resulting in more than one gas chromatography (GC) peak and thus reduced sensitivity. Generally, if two fragment ions are observed that are 28 mass units apart, then 57 (C 4 H 9 ) is added to the highest fragment ion to deduce the molecular weight of the TBDMS derivative. Identification is easily accomplished if mass spectra of the AAs are added to the computer-assisted library search routine. Accurate mass SIM reduces chemical noise at the expense of transmitted ion current. Mass spectra of TBDMS derivatives of PTH-Amino Acids Multiple TBDMS derivatives may form depending on the R group of the AA and the reaction time. The molecular ion is usually not observed but can be deduced by adding 87 (COOC 3 H 7 ) Daltons to the most abundant, high-mass ion. Masses 69 (CF 3 ) and 119 (C 2 F 5 ) may also be observed.

Chapter 29 – Prostaglandins (MO-TMS Derivatives)

This chapter discusses prostaglandins. Under derivatization (MO-TMS), the chapter explains that one has to evaporate the sample extract to dryness with clean and dry nitrogen. Then, the dried extract has to be stored at dry-ice temperatures until the sample is derivatized. The molecular ions of the MO-TMS derivatives are usually of low intensity but are detectable. Characteristic fragment ions are M-15 and M-31, with the M-31 ion being more abundant. The M-31 ion is intense only for ketoprostaglandins. By plotting the masses of the proceeding fragment ions, the presence or absence of a particular prostaglandin can be determined even though complete gas chromatography (GC) resolution may not be obtained. For the Prostaglandin PGA₁-MO-TMS (MW = 509), the Characteristic Abundant Ions are m/z 388, 419, 438, 478, and for the Prostaglandin PGE 1 -MO-TMS (MW = 599), the Characteristic Abundant Ions are m/z 426, 478, 528, 568, 584. Similarly for the Prostaglandin PGFl 1 -TMS (MW = 644), the Most Abundant Ions are m/z 367, 368, 438, 483.

Chapter 8 – Amines

This chapter deals with amines. MTBSTFA is the recommended reagent for silylating the amine functionality because it forms a more stable derivative than MSTFA, BSTFA, or BSA. Organic compounds with an odd number of nitrogen atoms will have an odd-mass molecular ion and prominent fragment ions at even masses. Underivatized diamines are difficult to identify by their mass spectra alone because of the low abundance of the molecular ion ( m/z 44, 58, or 72, and so on. If the unknown amine reacts with acetone or methyl-8, then it is a primary amine. With secondary amines, cleavage of the bond 13 to the nitrogen atom occurs preferentially at the shortest hydrocarbon chain. In the mass spectra of amino alcohols, the m/z 30 peak is intense while the m/z 31 peak is of relatively low abundance. A method to determine the number of amino groups present in the molecule requires the formation of a TMS derivative with MSTFA, which silylates both hydroxyl and amino groups. The molecular ions of the unsubstituted phenols are present, but are smaller than the underivatized aminophenols.

Chapter 19 – Isocyanates

This chapter presents mass spectra of aliphatic isocyanates. The general formula of aliphatic isocyanates is RNCO. The molecular ions of aliphatic isocyanates are observed up to C 8 . Characteristic fragments of aliphatic isocyanates include: m / z 56 (CH 2 NCO), 70 (CH 2 CH 2 NCO), and 84 (CH 2 CH 2 CH 2 NCO). Mass spectra of aromatic isocyanates, is discussed in the chapter. The general formula of aromatic isocyanates is ArNCO. The molecular ions of the aromatic isocyanates and diisocyanates are usually always observed, depending on the length of the alkyl groups on the ring. Losses from the molecular ion include: m / z 28 (CO), 29 (H + CO), and 55 (CO + HCN). Sometimes loss of hydrogen is observed, particularly if there is a methyl group on the ring. Gas chromatography (GC) separations of toluene diisocyates (TDI), xylene isocyanates, chloro-TDI, bromo-TDI, dichloro-TDI, and trichloro-TDI are discussed in the chapter. Gas chromatography separations of m -phenylene-diisocyanate, toluenediisocyanate, xylenediisocyanate, butylated hydroxytoluene, 5-chlorotoluenediisocyanate, methylene-bis-(4-cyclohexylisocyanate), and xylene diisocyanates are also discussed.

Chapter 10 – Common Contaminants

This chapter presents contaminants occasionally observed after derivatization with TMS reagents. Several contaminants occasionally observed in underivatized samples are presented in the chapter. Gas spectroscopy (GC) column bleed is a frequently encountered contaminant of mass spectra when high column temperatures are employed. Modern data systems offer the best way to eliminate this type of contamination by subtracting a spectrum showing column bleed from all other spectra in the gas spectroscopy (GC)/mass spectroscopy (MS) run.

Chapter 23 – Nitrogen-Containing Heterocyclics

This chapter focuses on the gas chromatography (GC) separations of nitrogen-containing heterocyclics and mass spectra of nitrogen-containing heterocyclics. The molecular ion of pyridines, quinolines, and acridines are usually abundant except when long-chain alkyl groups are attached to the ring. These are also known as Nitrogen-containing heterocyclics that lose HCN and H 2 CN from their molecular ions. A test for the presence or absence of the C-alkyl derivatives can be determined by preparing a TMS derivative. An alkyl group will be attached to the nitrogen atom, if the TMS derivative cannot be prepared. Alkyl pyrazines lose RCN from their molecular ions when the alkyl group is attached to the carbon adjacent to the nitrogen atom. Imidazole has an abundant molecular ion at m/z 68 but loses H and HCN to yield intense ions at m/z 67 and m/z 41. A characteristic fragment ion for alkylbenzimidazoles occurs at m/z 132.

Chapter 31 – Steroids

This chapter focuses on steroids. While discussing derivatization of steroids, the chapter provides the method for the preparation of TMS Derivatives and methoxime (MO)-TMS derivatives (especially for hydroxyketosteroids, which may decompose under the given gas chromatography (GC) conditions unless the MO-TMS derivatives are prepared). Molecular ions are usually observed for steriods that are sufficiently volatile to be analyzed underivatized by GC/ mass spectrometry (MS). Some important steroids in urine include estrone, estradiol, estriol, pregnanediol, and 17-ketosteroids, which can be analyzed by GC/MS as the TMS or the MO-TMS derivatives. It is possible to determine the elemental composition of the side chains of steroids by the difference in the mass between the molecular ion and an intense ion more than 15 Daltons below the molecular ion. The molecular ions of MO-TMS derivatives are generally more intense than the TMS-only derivatives. If two high-mass ions are observed that are 16 Daltons apart, add 31 Daltons to the more intense ion and 15 Daltons to the highest mass ion to deduce the molecular ion. By subtracting 29 Daltons for each keto group and 72 Daltons for each hydroxyl group, the original molecular weight of the steroid can be determined.

Chapter 30 – Solvents and Their Impurities

This chapter focuses on solvents and their Impurities. Generally, there are two types of analyses that are requested with reference to solvents. The first is the identification of residual solvents in products, and the second is the identification of impurities in common industrial solvents. Certain gas chromatography (GC) conditions have been found to separate most of the common solvents. The isomers may not be detected by this approach if they are not separated. In discussing mass spectra of solvents and their impurities, the chapter explains that solvents and their impurities represent a wide class of compound types; therefore, a discussion of common mass spectral features is meaning-less. The chapter lists the GC Separations of impurities in industrial solvents under capillary columns and packed columns.

Chapter 4 – Acids

This chapter focuses on acids. Krebs cycle acids have been analyzed using only the TMS derivatives, even though some are keto acids. 1 ml of urine is adjusted to pH 8 with NaHCO 3 solution. After that, methoxime hydrochloride or ethoxime hydrochloride is mixed and the solution is saturated with NaCl. Acids are found as many as 100 gas chromatography (GC) peaks in urine samples, which include urea and other non-acids. Although carboxylic acids are more often analyzed as methyl esters, there are occasions when they are more easily analyzed as free acids—such as in water at the ppm level. The mass spectrum of an acid can be distinguished from that of an ester by examining the losses of OH, H 2 O, and COOH from the molecular ion of acids in contrast to the loss of OCH 3 in the case of methyl esters. The molecular ion appears to be at m/z 172. Subtracting 32 for the two, oxygen of the carboxylic acid group leaves 140 Daltons.