Biomarkers - occurrence, utility, and detection - ACS Publications

Aug 1, 1988 - Phytoremediation of Petroleum Hydrocarbon–Contaminated Soils in Venezuela. Carmen Infante , Ismael Hernández-Valencia , Liliana López ...
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R. Paul Phllp and Jung-Nan Oung Schwl of Geology and Geophysics Unlvmity of Oklahoma Nwman, OK 73019

The study of natural products in plants, animals, bacteria, fungi, and other living systems has long been of interest to chemists, biochemists, and analytical chemists. Generally, however, these scientists are concerned only with the isolation and identification of compounds present in living systems. A relatively small but rapidly growing scientific discipline has emerged over the past two decades involving scientists primarily interested in the fate of organic material and associated natural produds after their demise and deposition in the sedimentary record and conversion into fossil fuels or "chemical fossils." Organic compounds present in the original source material whose carbon skeleton is preserved throughout the geological record are referred to as biomqkers. In this REPORT we will introduce some of the basic concepts of petroleum geochemistry and the key role that analytical chemistry has played in the development of this discipline. We will also discuss areas in which geochemical research is most likely to develop in the next few years, and we will

REPOR7 examine the major analytical challenges the organic geochemistwill meet in conducting geochemical research during the next decade. Aquatic environments such as swamps, lakes, deltas, and the ocean8 serve as a sink for dead and decaying organic material derived from living systems. Under appropriate environmental conditions (preferably reducing conditions), a small proportion of this organic matter, derived from carhon incorporated from atmospheric C02 via the photosynthetic cycle, will be preserved, and an even smaller proportion will maintain its integrity through0003-2700188/0360-887A/SO 1Sol0 @ 1988 Amerlcan Chemical Societv

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out several million years of the geological record. Indeed, remnants of organic debris and specific organic molecules have been found in rocks dating back to the Early Precambrian period (2-3 billion years ago). As shown in Figure 1, fossil fuels result from the leakage of small amounts of organic carbon from the photosynthetic cycle. This carbon, in the form of dead and decaying organisms, will be preserved if it is deposited in a reducing-type environment. Under appropriate conditions of temperature and pressure, this organic material can be converted into fossil fuels. In general, only about 0.01-0.1% of the organic material deposited into aquatic environments is actually incorporated into the sedimentary record. The remainder is rapidly oxidized, and the resulting COz returns to the atmosphere, where it again joins the photosynthetic cycle and is available to be re-incorporated into living systems. The photosynthetic cycle is selfreplenishing, although in time there is a slight reduction in the amount of COz directly returned to the cycle because some is incorporated into the sedimentary record. However, dissolution of naturally occurring carbonates, as well as other mechanisms, can maintain the balance of C02 in the atmosphere. Recently, additional COz has also been returned to the atmosphere by extensive burning of fossil fuels. This additional flux of COz has dist u b e d the fine balance of nature and resulted in the so-called greenhouse effect. Scientists interested in studying dead and decaying organic material after it has been deposited into the sedimentary environment include organic chemists, analytical chemists, microhiologists, paleontologists, geologists, 887 A

(6.4x 1Ot5 tons organic carbon)

and geochemists. One reason for this diverse interest is that fossil fuels are commonly accepted as having a biogenic orgin. This idea grew from the work of the famous German chemist Alfred Treibs, who in the late 1920s and early 1930s demonstrated a structural similarity between naturally occurring chlorophylls and porphyrins in crude oils. Treibs's proposal was recently confirmed using modern analytical techniques, and it has heen partly responsible for the development of the so-called hiomarker concept. In the late 1960s Egliiton and Calvin developedthe idea that when certain naturally occurring compounds are deposited in the sedimentary environment and undergo changes resulting from diagenesis and maturation, they lose their functional groups but their basic carbon skeleton remains intact. Hence it is possible to establish precursor-product relationships between naturally occurring compounds and their hydrocarbon analogues that were present in ancient sediments and crude oils. Such relationships permit these compounds, referred to as biomarkers, to provide information about the type of organic material responsible for a particular oil and about the geochemical history of a rock or oil.

Blomalker delermhaHon The determination of the organic compounds in crude oils or in extracts from source rock, coals, or oil shales provides a challengeequal to that found in virtually any other area of analytical chemistry. The method of choice for analyzing the complex mixtures obtained from such samples bas generally been gas chromatography (GC) and gas 888A

chromatographyhnass spectrometry (GCIMS). Most crude oils and source rock extracts produce chromatograms dominated by n-alkanes. These n-alkane distributions permit one to distinguish gross differences hetween the types of source materials responsible for a sample and to determine possible alteration from biodegradation, possible effects of migration, and relative maturity of the sample. For example, higher plant waxes predominantly show indigenous n-alkanes in the CW C s region with a marked dominance of odd- and even-numbered alkanes. Marine-derived material, on the other hand, is generally dominated by CnCZOalkanes. A number of processes can alter the distribution of these biomarkers after

they have heen incorporated into the geological record. Biodegradation of an oil initially removes lower carbon number alkanes and gradually removes those in the higher molecular weight 'regions. Shorter chain n-alkanes migrate far more rapidly than longer chain n-alkanes, leading to the enhancement of the former in oils that have migrated the greatest distances. The overall effect of maturation is to reduce both the marked odd-even dominance of the n-alkane distribution commonly ohserved in samples of low maturity and the naturally occurring materials such as plant waxes, until a smooth distribution of n-alkanes is obtained. The odd-even predominance (or carbon preference index) of n-alkanes can be used to determine the relative maturity of source rocks and, to a more limited extent, oils. The geochemical information obtained from n-alkane distributions in the early, developmental stages of geochemistry has been overshadowed recently by data obtainable from structurally more complex hiomarkers such as isoprenoids, steranes, terpanes, and porphyrins (see box). Although these classes of biomarkers provide far more geochemical information than n-alkanes, they are present in mixtures a t much lower concentrations and far greater complexity than the n-alkanes. Hence, more sophisticated analytical schemes are required for their determination, compared with the relatively routine GC techniques used for determination of n-alkanes. Analytical schemes in geochemistry, as in any other area of research, are tailored to suit the needs of an individual problem. After an organic-rich rock has been crushed and extracted with organic solvents, the extract is treated in much the same way as an oil. The

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Figure 2. Oil or source rock extract chromatograms. la1 Chmmarogramdominated by +alkanes. (b) Chromatogram dominated by branohed and EYCUC alkane8 after n.alkana, are removed by molecular sieving. R = pristine; m = phytane.

ANALYTICAL CHEMISTRY, VOL. 60, NO. 15, AUGUST 1, 1988

first step generally includes removal of the high molecular weight polar asphaltene fraction by precipitation with n-pentane. The asphaltene fractions can be characterized by techniques such as microscale pyrolysis-gas chromatography (py-GC) and py-GC/MS. Components remaining in the extract at this stage are dominated by hydrocarbons and more polar heteroatomic components. Fractionation of this extract can he achieved by thin-layer chromatography (TLC) or high-performance liquid chromatography (HPLC), which permit separation of the hydrocarbons into saturated and aromatic fractions. Until recently, most of the attention in geochemistry has been directed toward hydrocarbons in the carbon number range below C ~ O(There . are a variety of reasons that can be advanced for the interest in this molecular weight range, and some of these will be discussed later.) Analysis of the saturated fractions at this stage would generally produce gas chromatograms dominat ed by the n-alkanes, as mentioned above. The n-alkanes can be readily removed by either urea adduction or molecular sieving, leaving behind a fraction dominated by the branched and cyclic hydrocarbons (Figure 2). Research into the composition of thii fraction has been a dominant feature of organic geochemistry for the past decade. Despite the apparent simplicity of its gas chromatogram, this fraction is in reality a complex mixture of several hundred compounds. As a result of extensive research into this fraction from different oils and rock extracts, many well-characterized classes of biomarkers are now known to be present in most geochemical samples.

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sleranes and tarpanes Steranes and triterpanes are two classes of biomarkers that have been studied extensively in samples ofgeochemical interest. Typical sterane and terpane distributions present in a crude oil, as determined by monitoring their characteristic ions at mlz 217 and 191, are shown in Figures 3 and 4, respectively. Data obtained from these chromatograms for an oil or source rock can provide information on the nature of the original source material, relative maturity, and depositional environment. For oils, these data indicate relative migration distances and whether or not the material +been biodegraded. Steranes derived from sterols presentinlivingsystemswillbeusedto illustrate some of these applications. It is well documented that marine organisms generally have high concentrations of Cz7sterols that are converted to CZ, steranes through a series of complex diagenetic and thermal reactions. Similarly, higher plants contain ANALYTICAL CHEMISTRY. VOL. 60, NO. 15, AUGUST 1, 1988

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Figure 3. Sterane distributions in crude oils determined by single ion monitoring of m/z217. The resuHing diSblbUtlon wn6ists of regular and rearranged Sleranes. some of which have similar retention limes. The stereochemislry of the CIS stemnes 1s ahown on me peeks wrresponding lo lhese

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high concentrations of Czssterols that will give Czssteranes. (Recent work, however, has shown that certain algae also contain abundant CZSsterols.) The ratio of the Cn/Czssteranes has been used to indicate the relative amount of marine vs. higher plant source material present in a particular sample. In certain cases, specific steranes have been associated with a particular class of organism. For example, dinoflagellates contain an abundance of 4-methylsterols, which will produce 4-methylsteranes. Steranes possess a number of carbon atoms a t which the configuration of the

hydrogen atom can change as the maturity of the samples changes. Most sterols have a A5 double bond which, as a result of early diagenetic reduction, will lead to stanols and steranes with a 5a(H)/58(H) ratio that is usually greater than 3 to 1. This ratio will increase even further as maturity increases, leading to a dominance of the 5 4 H ) Configuration. The stereochemistry of the hydrogen atoms a t Clrand C1,also changes from the 14u(H), 17a(H), or aa configuration to the 88 configuration with increasing maturity. The 20R configuration, present in naturally occurring sterols, is transformed to 20s

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Flgure 4. Terpanes determined by single ion monitoring of m/z 191. The chmmalopmconsists ot mcyclic (numbers wim Wree symbols) and pentacyclictsmanes.gam macBrane (G). and 78a(H).oIeam (0). ;iRCLE 125 Oh READER SERVICE CAR1

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ANALYTLAL CHEMISTRY. VOL. 60, NO. 15. AUGUST 1. 1988

until an equilibrium value is reached for the ZOSIZOR ratio of approximately 0.54. The outcome of all these stereochemical changes is the production of a complex mixture of steranes and socalled rearranged steranes, as shown in Figure 3. Several scales based on relative concentrations of different sterane isomers have been proposed to permit determination of maturity information. The most commonly used are the 20S/(ZOS 20R) ratio and the relative proportions of the aa/(aa + 88) Cm steranes. Biodegradation of crude oils can alter their sterane distributions, and the first steranes to he removed when an oil is biodegraded are those with the naturally occurring 2OR stereochemistry at the CzOposition. As the extent of hiodegradation increases, all of the regular steranes are removed until ultimately only the rearranged steranes remain. A typical crude oil terpane distrihution is shown in Figure 4. Terpane distributions can provide a great deal of information complementary to that derived from sterane distributions. The major components in this chromatogram are the tricyclic and pentacyclic terpanes. This sample also contains high concentrations of gammacerane and 18a(H)-oleanane.The appearance of gammacerane in samples predominantly derived from hypersaline lacustrine environments, and to a lesser extent from marine environments, has made it a useful indicator for these environments. On the other hand, 18a(H)-oleanane is a useful biological marker indicative of an input from the higher plant angiosperms. The abundant pentacyclic terpanes in geochemical samples are the hopanes, derived predominantly from the C35 tetrahydroxyhopane, which serves as a cell wall rigidifier in prokaryotic organisms. Early work on this class of compounds was concerned with the basic pentacyclic molecule in the C27-C35 range. However, it has now been shown that an extensive array of hopanoids occurs in geochemical samples from various types of environments. These include thiohopanes, secohopanes, aromatized hopanes, and, most recently, various hexacyclic hopanoid derivatives present in samples from carhonate environments (see box on p. 889 A). The great diversity of these components has made them extremely important in interpreting various aspects of the geological record. It is impossible to exhaustively describe the significance of all biomarkers that have been identified in oils and source rocks, hut additional examples can he found in the list of suggested reading.

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ANALYTICAL CHEMISTRY. VOL. 60. NO. 15. AUGUST 1, IS88

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ronments, extent of biodegradation, and relative migration distances, the biomarker fiigerprints have another important function. When an oil accumulation is discovered, it is important from an exploration point of view to establish both the locations of the possible source rocks for the oil and of other accumulations from the same source rocks. If the source of an oil can be established, migration pathways to the reservoirs can be determined and a search can be made for additional accumulations of oil between the initial discovery and source area. If several oils have been discovered in one area, it is important to determine whether the oils are genetically related. One of the most successful methods developed for making oil-oil or oilsource rock correlations uses biomarker distributions. GC/MS is used to determine biomarker distributions, and then the chromatograms are compared to determine similarities or differences between them. Two samples of similar maturity and burial history will have similar biomarker distributions only if they had similar inputs of source materials, which, in turn, contain similar distributions of the biomarker precursors. In the past decade, a great deal of emphasis has been placed on the qualitative correlation of these biomarker fingerprints. Currently, an effort is also being made to introduce a quantitative aspect to this correlation approach. This is not a simple process, because different biomarker families are determined from a variety of different chromatograms and all will have different response factors. Hence there is no one internal standard that can be used for all classes of biomarkers.

Linked scarmhg mass spectral

methods A parallel for future developments can be drawn with the events of the past decade. Following the commercial availability of combined GC/MS systems and their associated data systems 10-15 years ago, research in geochemistry underwent a quantum leap of activity. This major advance in our analytical capability provided a significant impetus for the discovery and identification of biomarkers. In the past year or so, the commercialavailability of triple-stage quadrupole (TSQ) mass spectrometers and the development of new MSIMS techniques appears to have provided the stimulk needed to catalyze development of new approaches for the analysis of complex geochemical mixtures, particularly in the frontier areas of biomarker chemistry above the C ~ region. O The observation of unimolecular fragmentation reactions in the first field-free region of tandem sector instruments and collision-induced re-

actions in the TSQ have provided an excellent method for the analysis of complex mixtures. Numerous articles published recently in ANALYTICAL CHEMISTRYdescribe instrumentation and principles of operation of the TSQ and other hybrid mass spectrometers (see suggested reading list). This basic information will not be repeated here, but we will illustrate how the availability of such systems has already made an impact on geochemistry research. For example, Figure 3 shows that the distribution of steranes in a crude oil as determined from the single ion monitoring of mlz 217 is a complex mixture consisting of regular and rearranged steranes in the C27-c30 range. Because many of the homologues and isomers overlap, it is desirable to resolve components with the same carbon number from the total mixture. This can be achieved by operating the TSQ in the parent mode and observingthe sterane parent ions of the mlz 217 daughter ion (Figure 5). In this example, the Cn, CZS.and C29 members of the series have been resolved such that relative concentrations of various isomers with the same carbon number can be measured. This allows determination of maturity and accurate assessment of the relative amounts of CZ7, CZS,and CB steranes. A similar approach can be used to separate the tricyclic terpanes from the pentacyclic terpanes using the daughter ion a t m/z 191 and the respective series of molecular ions. Tricyclic terpanes have two degrees of unsaturation less than the pentacyclic terpanes, and it is a relatively simple task to separate them by making use of this difference. These are but two examples of the use of MSIMS in geochemistry. Several others, which illustrate initial attempts at applying this technique to these types of problems, have appeared in the recent literature (see- suggested reading list). The TSQ can also obtain a dauehter spectrum o> a specific parent ionthat has been separated mass spectrometrically from a complex mixture of other ions. In Figure 6, analysis of an oil from southeast Asia shows several peaks in the m/z 217 single ion chromatogram that do not appear to correspond to any previously identified steranes. From parent-daughter ion experiments, it could he established that one of these compounds had a molecular weight of mlz 412. When the sample was reanalyzed in the daughter mode and only the m/z 412 parent ion permitted to enter the collision cell to produce the collision-activated decomposition (CAD) spectrum shown in Figure 6, comparison with a previously published E1 spectrum and the component allowed identification of the C3,, terpane bicadinane.

882A * ANALYTICAL CHEMISTRY. VOL. 60, NO. 15, AUGUST 1. I988

Figure 5. Resolution of sterane distribu-

tions. (a) Total 81emna diswibution,(b) CII Smrane diatribution. (c) C2. slgime dirtribution. (dl Ca slerane

diswlbutlon.

The ability to rapidly switch between the parent and daughter operational modes of the TSQ greatly enhances the analytical power of this system. Figure 7a shows a partial chromatogram resulting from the determination of the pentacyclic terpane parents of mlz 191. Daughter ion analyses are performed along with parent ion analyses, and a t the end of the experiment the data system is used to deconvolute parent and daughter data. Figure 7b shows the chromatograms obtained by acquiring daughter spectra of parent ions a t m/z 398 and 412. Comparison with the data in Figure 7a establishes that the peaks labeled A and B have parent ions a t mlz 412 and 398,respectively. Complete daughter spectra of components A and B are also available (Figure 7c). Component B is 17cdH)norhopane, although component A remains as a CWunidentified pentacyclic terpane at this time. Operation in the parent mode demonstrates the presence of two co-elut-

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ing components that have parents a t mlz 398 and 412 and the alternating daughter experiments provide good daughter spectra on both components without the need for any background suhtraction, which assists in their identification. It is impossible to get this amount of information during one analytical run with a single-stage mass spectrometer, which again illustrates the advantage of using a tandem mass spectrometer for this type of analytical prohlem. An important application of hiomarker distributions has been, and will continue to be, the determination of oil-oil and oil+ource rock correlations. In many instances it is desirable to screen samples rapidly rather than undertake time-consuming fractionation processes followed by detailed GC and GC/MS analyses. Introduction of a sample via the direct insertion prohe into a TSQ operating in the parent mode permits one to analyze whole oils or hydrocarbon fractions directly, without any prior gas chromatographic separation, by monitoring a number of specific parent-daughter ion relationships. Because it is impossible to resolve various isomers, the amount of information ohtained is not as detailed as that obtained by GC/MS. It is possible, however, to obtain fingerprints for several claases of biomarkers from each direct insertion probe analysis; these can then he used to make either oil-oil or oil-source rock correlations. The distributions of steranes and tricyclic and pentacyclic terpanes obtained in this way for two oils are shown in Figure 8. Each molecular ion peak for the steranes consists of several regular and rearranged sterane isomers. However, the distribution of the molecular ion peaks a t mlz 312, 386, 400, and 414 permits one to see the relative proportions of the total CZ7, CB, Cpa and CW steranes-information that is useful for source determination. In addition, from the distrihution of the terpane parent ions, it is possible to determine the relative proportions of tricyclic to pentacyclic terpanes, a ratio that has been used to obtain information on relative migration distances. This rapid analysis of unfractionated samples will aid in the development of rapid oil-oil or oilsource rock correlation techniques. The ability to analyze whole oils or hydrocarbon fractions with the TSQ introduces another potentially important area of research in geochemistry: the search for novel biomarkers with molecular weights above that of CU,. This prohlem can be approached in two ways. In the past year or so, fused-silica gas chromatographic columns that are coated with aluminum have become available. These columns have much greater stability at high temperatures 894A

(up to 400-450 "C), allowing fractions of crude oils and source rock extracts to he analyzed when the majority of components are above CU,and range up to CIW.Preliminary data have shown the presence of n-alkanes with carbon numbers up to a t least C ~ Wwhich , implies that one might expect to find additional and more complex biomarkers in this molecular weight range as well. The second approach is to introduce the samples into the ion source via the direct insertion probe with the TSQ operating in the parent mode. This approach takes advantage of the fact that it is possible to distill these high molecular weight hiomarkers directly off the probe into the ion source and, hy using the system in the parent-daughter mode, obtain tentative identification of many of these molecules. Indeed, some of our preliminary results have provided tentative evidence to show that the hopanes extend up to at least C70 and probably higher. Similar results have been obtained for other

groups of biomarkers, and it is apparent that one of the major areas of geochemical research in the next few years will be the extension of biomarker geochemistry in the molecular weight ranges above 500 and up to 2000. In retrospect, there is nothing out of the ordinary about such a proposal if one considers what has happened in other fields of analytical chemistry. In the biochemical and biomedical fields, there has been a constant push toward the identification of higher molecular weight components in various types of biochemical fluids. We are now experiencing the initiation of similar efforts in geochemistry. From a geochemical standpoint, there are many reasons why it is advantageous to enter into high molecular weight range analysis. One of the important goals of geochemistry has been to develop precursorproduct hiomarker relationships that can be used for a variety of purposes, including determination of source materials. In general, it has been found

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Figuro 8. Dlatributlons of steranes (- - - -), tricyclic terpanes (-), and PentacyClic terpanes (- -) in oil using the direct insertion probe with the TSO operating in the parent mode.

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ANALYTICAL CHEMISTRY, VOL. 60, NO. 15, AUGUST 1. 1988

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that the larger and more complex the biomarker being investigated, the more useful it will be for providing geochemical information concerning source, maturity, extent of biodegradation, and depositional environments.

concluslaar This REPORT has introduced the concept of biomarkers and its application to organic geochemistry, particularly petroleum exploration. However, it is important to realize that the use of biomarkers is equally applicable to many other areas of geochemistry. These areas include the study of recent sediments and the association of functionalized hiomarkers with specific inputs of organic material and the use of specific hiomarkers as paleothermometers. In the latter approach, it has been found that the growth of certain organisms will vary with water temperature. Long-chain ketones are a characteristic feature of some of these organisms, and hence their concentrations in the sediments will also vary as a function of water temperature at the time.of deposition. Biomarkers have also been useful for fingerprinting the source of oil spills and other organic wastes and determining the source of this pollution. Biomarker determinations provide an intriguing challenge for the analyti-

cal chemist. Many common classes of hiomarkers can be readily determined by GCIMS and multiple-ion detection. However, the availability of hybrid instruments such as the TSQ has introduced a number of alternative methods for hiomarker determinations. Furthermore, the search for biomarkers can now be extended into the C4i,-Clw range with the TSQ operating in the parent mode. Until recently, most biomarkers identified in fossil fuels and related materials were hydrocarbons. However, researchers are increasingly interested in identifying sulfur- and nitrogen-containing species in these materials. Along with the search for novel higher molecular weight biomarkers, identifying these species will probably be a dominant part of geochemical research in the next decade. In addition to providing information on source, maturity, migration, and biodegradation, the correlation of specific hiomarkers with particular types of depositional environments will continue to develop as another important area of geochemical research.

I 5 8 A-I68 A.

Johnson, J. V.; Brittan, E. D.; Yost. R.A. Anal. Chem. 1986,58,132&29. Kondrat, R. W.; Cooks, R. G . A d . Chem. l978,50,81 A-92 A.

Mackenzie, A. S. In Advances in Petroleum Geochemistry 1984; Brooks, J.; Welte, D. H., Eds.;AcademicPrees:London;Vol. 1, pp. 115-214. McLafferty. F. W. Tandem Mass Spectrometry; Wiley: New York, 1983, p. 506. Philp. R. P.;,Lewis. C. A. Ann. Re". Earth Planet. Sei. 1987,15,363-95. Summons, ,R. E.; Powell, T.G. Geochim. Cosmochrm. Acta 1987,51,55746. Tissot, B.; Welte, D. H. Petroleum Formation and Occurrence, 2nd ed.:. Sorinrer . Verlag: Heidelberg, 1984. Yost, R.; Enke, C. Anal. Chem. 1979. 51, 1251 A-1264 A.

Warburton, G.A.; Zumberge, J.E. Anal. Chem. 1983.55.123-26.

w e d reading Hoffmann. C. F.; Foster, C. B.; Powell, T. G.; Summons, R. E. Geochrm. Cosmochim. Acta 1987,51(10), 2681-99. Hunt, J. M. Petroleum Geochemtstry and

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Geology; Freeman: San Francisco; 1979. Johnson. J.; Yost, R. Anal. Chem. 1985.57,

ANALYTICAL CMMISTRY. VOL. 60. NO. 15. AUGUST 1. 1988

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ofpetroleumgeochemiatry at'the University of Oklahoma. He received a Ph.D. in organic chemistry from the University of Sydney, Australia, in 1972 and has held research positions a t the University of Bristol, the University of California a t Berkeley, and the Commonwealth Scientific and Industrial Research Organization, Sydney, Australia. His research interests center around the application of organic chemistry to fossil fuel research, including the detection of biomarkers in oils, coals, and oil shales by GCIMS and the characterization of source rocks, coals, and oil shales usingpyrolysis GCIMS. Jung-Nan Oung is a graduate student a t the University of Oklahoma. He received B.S. and M.S. degrees from the National Chung-Hsing University in Taichung, Taiwan. He is developing novel methods for biomarker determinations using tandem mass spectrometry.