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Ion mobility spectrometry (IMS) mass spectrometry (MS) centers on the ability to separate gaseous structures by size, charge, shape, and followed by mass-to-charge (m/z). For oligomeric structures,...

During the past 50 years mass spectrometry has advanced from a small molecule method to one critical to understanding biological processes. The ability to analyze compounds as large as protein complexes did not happen with any single invention, but occurred in steps. Thus, electrospray ionization can be traced to Zeleny (1917) and Dole (1968), but also to Colby and Evans (1973) with the demonstration of electrohydrodynamic ionization of organic compounds. Likewise, matrix-assisted laser desorption/ionization can be traced to early work with laser desorption by Mumma and Vastola (1972), and the importance of a matrix in analysis of nonvolatile compounds can be attributed to Barber et al. with the introduction of fast atom bombardment (1981). Here, we look back over the past 50 years at the development of desorption methods for the analysis of nonvolatile compounds and the associated attempts at understanding the mechanism by which solid or liquid phase compounds are converted to gas-phase ions.

A recent report found that negative ion atmospheric pressure photoionization (Ni-APPI) and direct analysis in real time (Ni-DART) ionize compounds by electron capture, dissociative electron capture, proton abstraction, and anion adduction. The authors of this report suggested that the common ionization of Ni-APPI and Ni-DART demonstrated that these techniques ionize a wider array of compounds than negative ion atmospheric pressure chemical ionization (Ni-APCI). Here we show that Ni-APCI, using the atmospheric sample analysis probe (ASAP) technique, in the absence of solvent vapors, ionizes the same and similar compounds by the same reported mechanisms. These results are supported by previous publications, which show that each mechanism is active for Ni-APCI. This work demonstrates that irrespective of the initial method of ionization, at atmospheric pressure, similar ion/electron-molecule chemistries prevail.

In order to understand better the pathways for transport of ammonium perfluorooctanoate (APFO) from a point source, a focused investigation of environmental media (water and soil) near a fluoropolymer manufacturing facility (Site) was undertaken. Methods were developed and validated at 2 microg kg(-1) [the limit of quantitation (LOQ)] in soil, and at 50 ng l(-1) in water. Environmental media were sampled from a public water supply well field located north of the Site, across a river. The data suggest that APFO air emissions from the Site are transported to the well field, deposited onto the soil, and then migrate downward with precipitation into the underlying aquifer.

The methodology for the determination of perfluorooctanoate (C(7)F(15)COO-, PFO), fluorotelomer alcohols (FTOHs: 6-2, 8-2, and 10-2), perfluorooctyl iodide (PFOI), and 8-2-8 fluorotelomer alcohol ester in complex fluorotelomer-based commercial products has been demonstrated and validated. Sample preparation procedures allowing determination of residual levels of these compounds were developed. The analytes were detected either by LC/MS/MS (PFO), LC/MS (FTOHs), or GC/MS (PFOI, 8-2-8 ester). The methods were validated by investigating the recoveries of analytes spiked at multiple levels to authentic sample matrices. The recoveries generally were between 70 and 130%. The limits of detection were in sub-microg/g range and the limits of quantitation were in the mug/g range. The methods were applied to fluorotelomer-based raw materials and fluorotelomer-based surfactants and polymeric products and represent methods useful for the determination of higher carbon chain length homologs as well.

To determine the optimum conditions for the complete extraction of perfluorooctanoate (PFO) from polytetrafluoroethylene fluoropolymers, sample preparation and pressurized solvent extraction (PSE) conditions were investigated. Solvent extraction temperature, solvent residence time, relaxation time between extractions, and the effects of heating before PSE showed that methanol at 150 degrees C extraction temperature and a 12 min solvent residence time were the most efficient conditions. Preheating the polymer before extraction at 150 degrees C for 24 h significantly enhanced the quantity of PFO removed. Heating above 150 degrees C resulted in loss of PFO. PFO was determined by liquid chromatography with tandem mass spectrometry.

The field of proteomics requires methods that offer high sensitivity and wide dynamic range. One of the strategies used to improve the dynamic range is sample prefractionation, such as microsolution isoelectric focusing (IEF). We have modified a commercial solution IEF instrument, the Rotofor®, to prefractionate protein mixtures by carrier ampholyte-free solution IEF. The focusing chamber of the Rotofor was divided into several compartments by polyacrylamide membranes with imbedded Immobiline mixtures of specific pH values. When an electric field is applied, each protein migrates to the compartment confined by membranes with pH values flanking its isoelectric point. The approach was demonstrated for the focusing of myoglobin into a predicted compartment, as well as the separation of a complex soluble yeast protein mixture into several distinct fractions. The proteins were dissolved in water or 30% isopropanol. The method is applicable to both gel-based and solution-phase protein identification methods, without the need for further sample preparation.

An automated sample preparation for high throughput accurate mass determinations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed. Sample preparation was performed with an automated workstation and automated mass analyses were performed with a commercial MALDI-TOF mass spectrometer. The method was tested with a 41-sample library. MALDI-TOFMS was found to give the needed sensitivity, accurate mass measurement, and soft ionization necessary for structure confirmation, even of mixtures. A mass accuracy of 5 ppm or less was obtained in over 80% of known compound measurements. A mass accuracy better than 10 ppm was obtained for all measurements of known compounds. Analyses of parallel synthesis products resulted in 77% of the measurements with a mass accuracy of 5 ppm or better. Copyright © 2000 John Wiley & Sons, Ltd.

Residual acrylamide can cause severe suppression of signal intensity during matrix-assisted laser desorption/ionization (MALDI) peptide mass mapping experiments. This suppression phenomenon can compromise the ability to detect low picomole and subpicomolar amounts of peptides extracted from two-dimensional gels. A rapid and simple method that exploits the use of pipette tips incorporating C18 packing materials for the enhancement of MALDI signal intensity is presented. The utility of the method is demonstrated with peptide solutions incorporating residual acrylamide and/or gel monomer components. Copyright © 2000 John Wiley & Sons, Ltd.

To elucidate the role of high mass accuracy in mass spectrometric peptide mapping and database searching, selected proteins were subjected to tryptic digestion and the resulting mixtures were analyzed by electrospray ionization on a 7 Tesla Fourier transform mass spectrometer with a mass accuracy of 1 ppm. Two extreme cases were examined in detail: equine apomyoglobin, which digested easily and gave very few spurious masses, and bovine alpha-lactalbumin, which under the conditions used, gave many spurious masses. The effectiveness of accurate mass measurements in minimizing false protein matches was examined by varying the mass error allowed in the search over a wide range (2-500 ppm). For the "clean" data obtained from apomyoglobin, very few masses were needed to return valid protein matches, and the mass error allowed in the search had little effect up to 500 ppm. However, in the case of alpha-lactalbumin more mass values were needed, and low mass errors increased the search specificity. Mass errors below 30 ppm were particularly useful in eliminating false protein matches when few mass values were used in the search. Collision-induced dissociation of an unassigned peak in the alpha-lactalbumin digest provided sufficient data to unambiguously identify the peak as a fragment from alpha-lactalbumin and eliminate a large number of spurious proteins found in the peptide mass search. The results show that even with a relatively high mass error (0.8 Da for mass differences between singly charged product ions), collision-induced dissociation can help identify proteins in cases where unfavorable digest conditions or modifications render digest peaks unidentifiable by a simple mass mapping search.

Elucidating structure function relationships of DNA in cellular processes requires fast, reliable methods that can be applied to picomole amounts of sample. Higher order structure can be inferred by distinguishing paired and unpaired regions. It is shown here that enzymatic digestion coupled with product analysis by matrix-assisted laser desorption ionization (MALDI) is able to identify unpaired bases within structured DNA regions. The method is demonstrated with DNA duplexes having a five nucleotide mismatch as a 5′ overhang, a 3′ overhang, and an internal loop. Exo- and endonuclease digestions are performed under solution conditions (temperature, annealing, and enzyme buffers) which promote base pairing and specific enzyme activity. For each type of mismatch, the length and sequence of the single stranded region can be inferred from MALDI spectra taken as a function of digestion time.

Size exclusion chromatography (SEC) isolation of affinity-selected ligands combined with reverse phase liquid chromatography-mass spectrometry (LC-MS) is an effective means for identifying members of mixtures which form tightly bound noncovalent complexes with target proteins. A potential liability of the approach is that the SEC isolation is carried out under nonequilibrium conditions favoring protein/ligand complex dissociation. At long SEC isolation times and/or for complexes with fast off-rates the extent of dissociation can jeopardize the ability to detect the affinity-selected components. Additionally, equilibrium binding affinities cannot be exactly determined from the measured distribution of isolated ligands. We present here an online SEC/LC-MS system for determining affinity-selected members of active mixtures which reduces this liability. A kinetic model of the SEC isolation process is developed to determine the practical limits for the application of the method and to extrapolate equilibrium binding affinities from the nonequilibrium data. The utility of online SEC/LC-MS for identifying affinity-selected ligands and for estimating binding affinities is demonstrated for a small molecule mixture of compounds with known binding affinities and for a simple combinatorial mixture.

Electrospray ionization-Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry allows for high-resolution, accurate mass analysis of multiply charged ions of proteins. In the work described here, the ability of ESI-FTICR to distinguish small differences in molecular mass is evaluated. Ubiquitin was used as an internal mass calibration standard to measure the molecular mass of cytochrome c, myoglobin, and several carbonic anhydrase isoforms. Mass calibration was based on the tallest isotopic peak of each ubiquitin charge state. Ubiquitin performed well as an internal standard because its charge states covered the appropriate mass range, interference was minimal, and the tallest peak was easily identified. The peak masses of cytochrome c (12.5 kDa) and myoglobin (17 kDa) were measured to an accuracy of about 0.02 Da (2ppm). However, errors of 1.0 Da were observed for some individual determinations because of the difficulty in identifying the tallest peak. When the technique was applied to bovine carbonic anhydrase II, even combining data from several charge states did not yield an unequivocal assignment of the tallest peak, resulting in a mass assignment of 29,023.7 or 29,024.7. Similarly, measurements of two isoforms with a mass difference of 1 Da, human carbonic anhydrase I, pI 6.0 and 6.6, yielded overlapping values for the mass of the tallest peak. However, these two isoforms were clearly distinguished by (a) identification of the tallest peak using a measurement of average mass as a guide and (b) comparison of the isotopic peak intensity patterns.

Calf spleen phosphodiesterase cleaves oligonucleotide strands in a stepwise manner from the 5′ end and can be used in combination with matrix-assisted laser desorption ionization (MALDI) mass spectrometry to perform ladder sequencing. The relative intensities of ladder peaks in the mass spectra of a series of 5-mers and 7-mers show that the rate of digestion is influenced by strand sequence. Sequences terminating in A or G at the 5′ end are found to react two to three times faster than sequences terminating in C or T. The reactivity of the terminal base is also influenced by the sequence beyond the 5′ end. When the third base from the 5′ end is A or G, removal of the first and second bases is faster than when the third base is C or T. A method is described which permits reaction rates to be quantitatively determined from the time dependences of ladder peaks in the MALDI spectra. A similar approach could be used for mechanistic studies.

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (tof) mass spectrometry (MS) has been reported to give low number average and weight average molecular weight values for polymers of wide polydispersity. Spectra of wide polydisperse polymers more closely resemble the distribution observed by size exclusion chromatography when obtained in the reflectron mode. However, the highest mass molecules in the distribution are not observed. These high-mass ions can be observed when the more abundant lower mass ions are deflected from reaching the detector. In addition, a mixture of three narrow distribution polymer standards selected to provide a wide mass distribution do not show discrimination against the high-mass molecules. These results are interpreted to suggest that the difficulty in observing accurate molecular weight distributions by MALDI-TOF-MS is at least in part attributable to instrumental limitations rather than ionization limitations.

A dynamic method was used to determine the vapor pressures of perfluorooctanoic, -nonanoic, -decanoic, -undecanoic, and -dodecanoic acids. Measurements were made over the temperature range from (59.25 to 190.80) °C for perfluorooctanoic acid, from (99.63 to 203.12) °C for perfluorononanoic acid, from (129.56 to 218.88) °C for perfluorodecanoic acid, from (112.04 to 237.65) °C for perfluoroundecanoic acid, and from (127.58 to 247.36) °C for perfluorododecanoic acid. Pressures ranged from (0.128 to 96.50) kPa for perfluorooctanoic acid, from (1.12 to 99.97) kPa for perfluorononanoic acid, from (3.129 to 99. 97) kPa for perfluorodecanoic acid, from (0.616 to 99.97) kPa for perfluoroundecanoic acid, and from (0.856 to 99.96) kPa for perfluorododecanoic acid. A sealed vial experiment demonstrated that perfluorooctanoic acid sublimes at room temperature.

Molecular weight measurements of several oligonucleotides ranging in size from 12 to 60 bases were performed by matrix-assisted laser desorption/ionization with a time-of-flight mass spectrometer (MALDI-TOF). In each case, the mass accuracy was better than 0.1%. Sequences for two 12-base oligonucleotides and a 24-base oligonucleotide were determined using calf spleen phosphodiesterase to sequentially cleave from the 5' end. A MALDI-TOF spectrum of the digest mixture shortly after the addition of the enzyme produced a characteristic oligonucleotide ladder. Molecular ions in the mass spectrum corresponded to the products of enzymatic cleavage, and the mass differences between these peaks identified the individual nucleotides. The resolution and mass accuracy of MALDI-TOF were sufficient to unambiguously identify the individual nucleotides in the 12- and 24-base strands.

Matrix-assisted laser desorption/ionization mass spectrometry (MS) has been shown to provide most probable peak (Mp) values for poly(methyl methacrylate) polymers that are low relative to manufacturers, Mp values measured by size exclusion chromatography (SEC). Comparison of theoretical Mp values determined by MS or SEC is shown to be a function of how the data are displayed. For narrow polymer distributions, the theoretical Mp value determined by MS will be 2 monomer units smaller than the Mp determined by SEC. For wide polydispersity, the Mp value determined by MS will be considerably lower than those obtained from SEC. The Mp value reported should be reserved for weight fraction vs log mass plots as in SEC. The modal molecular mass, Mm, is recommended for data represented as number fraction vs linear mass as with MS data.

Multiply charged ions, similar to those obtained with electrospray ionization, are produced at atmospheric pressure (AP) using standard MALDI conditions of laser fluence and reflective geometry. Further, the charge state can be switched to singly charged ions nearly instantaneously by changing the voltage applied to the MALDI target plate. Under normal AP-MALDI operating conditions in which a voltage is applied to the target plate, primarily singly charged ions are observed, but at or near zero volts, highly charged ions are observed for peptides and proteins. Thus, switching between singly and multiply charged ions requires only manipulation of a single voltage. As in ESI, multiple charging, produced using the AP-MALDI source, allows compounds with molecular weights beyond the mass-to-charge limit of the mass spectrometer to be observed and improves the fragmentation relative to singly charged ions.

Cassini-Huygens ended its four-year prime mission on July 1, 2008. Significant challenges to developing and executing the science plan for the orbiter mission had to be overcome to return a wealth of science data from its tour of the Saturnian system. These operational challenges reflected the complexity of the mission, of the tour, of the spacecraft, of its instruments, and of the ground system environment. This paper discusses in-depth the lessons learned from the science planning operations of Cassini including the multi-step uplink process designed to select, integrate and implement science observations. Aspects of system engineering, spacecraft design, spacecraft subsystems, flight hardware and software, ground software, instrument and science operations that either facilitated or complicated science return are also addressed.

Electrospray mass spectra of carbonic anhydrase (MW ∼ 29000) and ovalbumin (MW ∼ 45000) were obtained on a double focusing magnetic secter mass spectrometer by using a single stage of mechanical pumping in the interface between atmospheric pressure and high vacuum. Full scan spectra of lysozyme were recorded on 15 fmoles consumed. In addition, accurate mass measurement was demonstrated for peptides and proteins, and resolution in excess of 10,000 (m/Δm, 10% valley) was observed. These results clearly show that high performance magnetic sector mass spectrometers can be advantageously interfaced to an atmospheric pressure electrospray ion source.

The feasibility of interfacing an electrospray ion source to a high-performance magnetic-sector mass spectrometer is demonstrated. Spectra of peptides and small proteins are obtained with good sensitivity, resolution and mass accuracy. The advantages of using a high-performance mass spectrometer in conjunction with electrospray ionization are discussed.

Sequence information is obtained by in-source fragmentation of electrospray-generated peptide ions. The complete sequences of leucine enkephalin, angiotensin I, and renin substrate are determined from their fragment ions and consume only low picomole amounts of material. The method involves collision-induced fragmentation of singly and multiply charged molecular ions in the electrospray ion source and does not involve tandem mass spectrometric instrumentation. The charge on the fragment ions is determined by the spacing of the isotope peaks.

The need to analyze perfluorinated-acid chains of various lenghts drives the demand for new analytic methods.

Direct analysis of samples using atmospheric pressure ionization (API) provides a more rapid method for analysis of volatile and semivolatile compounds than vacuum solids probe methods and can be accomplished on commercial API mass spectrometers. With only a simple modification to either an electrospray (ESI) or atmospheric pressure chemical ionization (APCI) source, solid as well as liquid samples can be analyzed in seconds. The method acts as a fast solids/liquid probe introduction as well as an alternative to the new direct analysis in real time (DART) and desorption electrospray ionization (DESI) methods for many compound types. Vaporization of materials occurs in the hot nitrogen gas stream flowing from an ESI or APCI probe. Ionization of the thermally induced vapors occurs by corona discharge under standard APCI conditions. Accurate mass and mass-selected fragmentation are demonstrated as is the ability to obtain ions from biological tissue, currency, and other objects placed in the path of the hot nitrogen stream.

This study demonstrates that 1,5-I-AEDANS (5-({2-[(iodoacetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid) can be used as a versatile fluorescence-based peptide quantification tool and provides readily interpretable tandem mass spectra for de novo peptide sequencing. Two AEDANS-cysteinyl-peptide fractionation strategies were evaluated. One AEDANS-cysteinyl-peptide fractionation strategy employs immobilized metal affinity chromatography (IMAC) to recover AEDANS-labeled peptides and reduce the complexity of peptide mixtures. In an alternate solid-phase approach, 1,5-I-AEDANS was coupled to an o-nitrobenzyl-based photocleavable resin to produce a resin that can label and isolate thiols and cysteine-containing peptides with a modified-AEDANS label (mAEDANS: 5-((4-amino-4-oxobutanoyl){2-[(iodoacetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid). This fractionation protocol enriches cysteine-containing peptides more specifically than the IMAC strategy. Using micro-LC-ESI-MS with an on-line fluorescence detector and a Q-TOF mass spectrometer, we generated fluorescence-based elution profiles and corresponding positive ion mass spectra of AEDANS-labeled peptides. This study demonstrates that AEDANS-peptides produce positive ion ESI-MS mass spectra with detection limits comparable to those of the unlabeled peptide. Collision-induced dissociation (CID) of fluorescent AEDANS-peptides revealed readily interpretable product ion spectra with the label intact. Similar to the AEDANS-labeled peptide, an mAEDANS-labeled thiol is fluorescent and CID of a mAEDANS-labeled peptide also reveals an interpretable product ion spectrum with the label intact.

Facile additions of alkyl radicals and hydrogen atoms to C{sub 60} are observed to occur in a mass spectrometer ion source. These reactions have not been reported previously even though mass spectrometry played an important role in the discovery of the novel C{sub 60} allotrope of carbon, and numerous mass spectrometric studies have since been reported for the various fullernes, including chemical-ionization (CI) and electron-attachment (EA) studies in which adduct ions were observed. On the basis of the mass spectrometric characterization of the radical products from the solution work by Krusic et al. and the discovery in this laboratory of compounds that efficiently trap radicals under CI conditions, the authors looked for radical additions to C{sub 60} occurring in the CI ion source of a VG 70SE mass spectrometer.

A calmodulin photo adduct was characterized using a combination of fast atom bombardment mass spectrometry, amino acid analysis and Edman sequence results. The C-terminus of the V8 digest and the specific residue of interaction of the photo adduct with calmodulin was identified.

This chapter discusses plasticizers and other polymer additives. The capillary columns include triethylcitrate (MW = 276), dibutylphthalate (MW = 278), dibutylsebacate (MW = 314), acetyltributylcitrate (MW = 402), trioctylphosphate (MW = 444), di-(2-ethylhexyl)adipate (MW = 370), di-(2-ethylhexyl)phthalate (MW = 390), and di-(n-decyl)phthalate (MW = 444) 15 m DB-1 column, 75–275° at 10°/min and the Dimethyl terephthalate impurities acetone (MW = 58), benzene (MW = 78), toluene (MW = 92), xylene (MW = 106), methylbenzoate (MW = 150), and CHO (C 6 H 4 )CO 2 CH 3 (MW : 164). NC-(C6H 4 )CO 2 CH 3 (MW =161), methyltoluate (MW = 150), p-nitromethylbenzoate (MW = 181), dimethylterephthalate (MW = 94), methyl DMT (MW = 208), CHsOC(O)-C 6 H 4 -CH(OCH 3 ) 2 and isomer (MW = 210), and CH 3 OC(O)-C 6 H 4 -C 6 H3-(CO 2 CH 3 ) 2 (MW = 328) 30 m DB-1 column, 100-250° at 10°/min also held characteristics of capillary columns under the influence of general condition. If the MW is not m/z 166 and there is an intense ion at m/z 149, this suggests an ester of a benzene dicarboxylic acid. If m/z 149 is the most intense ion, the mass spectrum represents a phthalate, where R is an ethyl group or larger.

This chapter discusses phosphorus compounds. The molecular ion is easily observed. A very intense fragment ion is observed at m/z 135 corresponding to [(CH 3 ) 2 N] 2 PO. Separations through capillary columns are found to be very useful for diverse phosphorus compounds. Mass spectra of phosphorus compounds include alkyl phosphites, alkyl phosphates, alkyl phosphonates, and phosphoramides. While experimenting, a very intense fragment ion is observed at m/z 135 corresponding to [(CH3)2N] 2 PO.

It is crucial in quantitative gas chromatography (GC) to obtain a good separation of the components of interest. Although this is not critical when a mass spectrometer is used as the detector, it is nevertheless a good practice. Because the response for any individual compound will differ, it is necessary to obtain relative response factors for those compounds for which quantitation is needed. Care should be taken to prevent contamination of the sample with the reference standards. This is a major source of error in trace quantitative analysis. To prevent such contamination, a method blank should be run, following all steps in the method of preparation of a sample except the addition of the sample. To ensure that there is no contamination or carryover in the GC column or the ion source, the method blank should be run prior to each sample.

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.

This chapter discusses the preparation of TMS derivatives of primary and secondary aromatic amides, as well as the preparation of acetate derivatives of primary and secondary aromatic amides. The mass spectra of underivatized amides generally show molecular ions. If the unknown mass spectrum has an intense peak at m/z 59 and an abundant m/z 72 with an odd molecular ion, this suggests a primary amide. The chapter highlights that the mass spectra of secondary amides have an intense rearrangement ion at m/z 30. In simple aromatic amides, fragmentation occurs on both sides of the carbonyl group. If hydrogen is available in N-substituted aromatic amides, it tends to migrate and form an aromatic amine and the loss of a ketene.

In pesticide extraction, for pesticide extraction procedures pertaining to food samples, it is better to refer to U.S. government manuals on pesticide residue analysis. The Environmental Protection Agency (EPA) has prepared a manual of pesticide residue analysis dealing with samples of blood, urine, human tissue, and excreta, as well as water, air, soil, and dust. The molecular ion is apparent in the mass spectrum of DDT at m/z 352 with the classic isotope pattern for five chlorine atoms. Trichlorofon loses HCl from the molecular ion, producing a spectrum identical to that of dichlorovos. These pesticides can be differentiated by preparing a TMS derivative.

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.

This chapter discusses the gas chromatography (GC) separations and mass spectra of halogenated compounds. GC separations are of two types: (1) saturated and unsaturated halogenated compounds and (2) halogenated aromatics. Capillary columns are mostly of dichlorobutenes and trichlorobutenes 30 m DB-Wax column, 70-200 degree at 4 degree/min. Packed columns have many halogenated compounds from methyl chloride to chlorobenzene 3 m Carbowax 1500 column on Carbopack C, 60 (4 min) – 170 degree at 8 degree per min. The presence of chlorine or bromine is detected by their characteristic isotropic patterns. Sample mass spectrum of aliphatic halogenated compound and aromatic halogenated compound is explained in the chapter. If an intense ion at m/z 91 is present, then the halogen is on the alkyl side chain. If the halogen is on the ring, the loss of the halogen from the molecular ion will result in a small peak. The intensity of the molecular ion indicates the presence of aromatic compound.

This chapter discusses the sulfur compounds. The presence of sulfur can be detected by the 34 S isotope (4.4%) and the large mass defect of sulfur in accurate mass measurements. In primary aliphatic thiols, the molecular ion intensities range from 5-100% of the base peak. Loss of 34 (H 2 S) Daltons from the molecular ions of primary thiols is characteristic. In secondary and tertiary thiols, 33 Daltons rather than 34 Daltons are lost from their molecular ions. If m/z 47 and 61 are reasonably abundant ions, and m/z 61 is approximately 50% of m/z 47, then the mass spectrum represents a primary thiol. If m/z 61 is much less than 50% of m/z 47, then the mass spectrum represents a secondary or tertiary thiol. Saturated sulfur compounds generally fragment beta to the sulfur atom to lose the largest alkyl group. Molecular ions are usually reasonably abundant. Cyclic thioethers give abundant molecular ions and an abundant fragment ion because of double β-cleavage. The thioethers can be distinguished from the primary, secondary, and tertiary thiols by the absence of the losses of either 33 or 34 Daltons from their molecular ions.

This chapter discusses the gas chromatography (GC) separation of ketones, derivatives of ketones, and mass spectra of ketones. The derivative of ketones is used to determine the presence and number of keto groups and it is used to protect the ketone from enolization. The ketone group can be reduced to an alcohol that can then be silylated. This procedure has been used to identify the keto group in carbohydrates. The four characteristics of aliphatic ketone, aromatic ketones, and cyclic ketones are general formula, molecular ion, fragmentation, and characteristic fragment ions. The MW of aliphatic ketones can be determined from its prominent molecular ion. Usually, the intensity of the molecular ions of ketones is greater for C 3 –C 8 than for C 9 –C 11 . Molecular ions of cyclic ketones are relatively intense. Ketosteroids are a special class of cyclic ketones and have abundant molecular ions. The molecular ions are always present in aromatic ketones.

This chapter discusses the gas chromatography (GC) separation of underivatized aldehydes, derivatization of formaldehyde, and mass spectra of aldehydes. Although the DB-FFAB column is similar to the DB-WAX column, it should not be used to separate aldehydes because it may remove them from the chromatogram. Formaldehyde is derivatized for trace analyses. Only selected ion monitoring of mass 127 is used to determine the concentration of formaldehyde. Both straight-chain and branched aliphatic aldehydes show molecular ion peaks up to a minimum of C 14 aldehydes. Aromatic aldehydes provide a very intense molecular ion. Accurate mass measurement data indicate the presence of an oxygen atom. Aldehydes are distinguished from alcohols by the loss of 28 and 44 Daltons from the molecular ion. The M-44 ion results from the McLafferty rearrangement with the charge remaining on the olefinic portion. The mass spectra of aliphatic aldehydes show m/z 29 (CHO) for C 1 –C 3 aldehydes and m/z 44 for C 4 and longer chain aldehydes.

An intense peak in the mass spectra of C 6 –C 26 methyl esters results from the McLafferty rearrangement. If even small peaks are observed at m/z 31, 45, 59, and so forth, then it is likely that oxygen is present. Unsaturation in an ester is normally apparent from the molecular weight and the more abundant molecular ion. The position of the double bond can be determined by locating two peaks that differ by 12 mass units. Mass spectra of pyrrolidine derivatives of methyl or ethyl esters also apply to the case when two double bonds are present with only a CH 2 group separating them. Interpreting the mass spectra of ethyl esters may be confusing without accurate mass measurement because the loss of C 2 H 4 can be confused with the loss of CO from a cyclic ketone. The methyl esters of aromatic cyano acids show intense molecular ions, but the intensity decreases as the length of the side chain increases.

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.

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.

This chapter discusses the gas chromatography (GC) separations and mass spectra of fluorinated compounds, which are referred to as “F-115.” To translate this code into a molecular formula, add 90 to 115. The first digit of the sum is the number of carbons; the second, the number of hydrogens; the third, the number of fluorines; chlorines complete the valences (i.e., C 2 F 5 C 1 is F-115 = 90 + 115 = 205, or CzHoFs). A four-digit number is used for unsaturated molecules. Intense molecular ions are observed in the mass spectra of fluorinated benzene, ethyl benzene, toluene, and xylene. The chlorofluoroaromatics can easily be identified by examining the isotope ratios near the molecular ion. The m/z 31 ion is frequently more abundant in fluorinated olefins than in fluorinated saturated compounds. Molecular ion is usually not observed with perfluorinated ketones, but may be deduced by adding 19 Daltons to the highest mass observed in the case of perfluoroacetone and 69 Daltons in the case of perfluorodiethyl ketone.

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.

Because drugs and metabolites are typically polar and thermally labile molecules, liquid chromatography/mass spectrometry (LC/MS) rather than gas chromatography/mass spectrometry (GC/MS) may be a more desirable approach. Urine extracts from rats exposed to OPD were examined without derivatization. The major metabolites were identified as methylbenzimidazole, methylquinoxaline, and dimethylquinoxaline. Drugs and metabolites can be extracted from cultures and urine by adding 2 drops of concentrated HCl to 1 ml of urine for a pH of 1–2. The mass spectra of metabolites will usually follow similar fragmentation pathways to those prevalent in the mass spectra of the precursor molecule. Thus, knowledge of the possible biotransformations that can lead to metabolites is important. By carefully examining the fragmentation pattern of the metabolite and comparison with the mass spectra of the precursor molecule, it is often possible to determine not only the nature of the biotransformation, but also its position in the molecule. Two major sources that are available for identifying drugs are (1) computer library search routines and (2) mass spectral and GC data of drugs, poisons, and their metabolites.

This chapter discusses the gas chromatography (GC) separation of derivatized sugars and mass spectral interpretation. Preparative methods of monosaccharides, amino sugars, sugar alcohols, and reduced sugars such as Acetates are also provided in the chapter. Generally, to deduce the molecular weight of the TMS derivative of sugars, add to 105 the highest mass observed. Comparison of GC retention times together with the mass spectra is sufficient to identify the sugars. Chemical ionization using ammonia as reagent gas establishes the molecular weights of sugar acetates. If m/z 204 is more abundant than m/z 217, the hexose is the pyranose form, but if m/z 217 is most abundant then it is a furanose. Aldohexoses is differentiated from ketohexoses by the ion at m/z 435 for aldohexoses versus m/z 437 for ketohexoses. By plotting out the molecular ion mass and mass 362.1639, the presence of these amino sugars can be determined. The mass spectrum of alditol acetates are easy to interpret as they fragment at each C–C bond.

This chapter discusses gas chromatography (GC) separation of nitriles and mass spectra of nitriles. The aliphatic mononitriles may not show molecular ions when R is greater than C 2 . If CH 3 is replaced by CF 3 , as in the case of CF 3 CH 2 CH 2 CN, fluorine is first lost from the molecular ion, followed by the loss of HCN. As the alkyl chain length increases, it is being diminished by the influence of CF 3 group. Adiponitrile may be distinguished from methylglutaronitrile by the relative intensities of m/z 41 and 68. If the abundance of m/z 68 is greater than that of m/z 41, the mass spectrum represents methylglutaronitrile. The loss of 27 (HCN) Daltons from the molecular ions of aromatic nitriles and dinitriles is characteristic. The tolunitriles show the losses of hydrogen, HCN, and H2CN. The loss of 19 (F) and 50 (CF 2 ) Daltons is very intense if the methyl group is replaced by a CF 3 group. If the nitrile group is on the side chain rather than on the aromatic ring, the loss of 27 (HCN) Daltons occurs.

This chapter discusses the gas chromatography (GC) separation of gases. Gases like O 2 , N 2 , CO, CO 2 , C 1 -C 5 hydrocarbons, low-boiling fluorinated compounds, sulfur compounds are used in gas analysis. Separating or passing the effluent from the GC column through a sensitive thermal conductivity detector (TCP) before entering the mass spectrometry (MS) enables the qualitative and quantitative analyses of unknown gas mixtures from ppm levels to percentage levels. If elaborate column switching systems are not available, two GC/MS runs may be required on two different columns. By performing two GC/MS runs on two different columns, a complete gas analysis can be achieved. If a sufficient number of analyses are made, the Molecular Sieve 5A column will have to be replaced. This column separates oxygen and nitrogen better than the Molecular Sieve 13X column. Packed columns contain carbon dioxide, sulfur dioxide, carbonyl sulfide, acetylene, and hydrogen sulfide along with 2 m silica gel column at room temperature.