What is Kovats Indices and How to Identify Biomarkers in GCMS (Hopane, Sterane, Coronene, Cadalene, Phenanthrene)


Oxygen-containing aromatic compounds (such as dibenzofuran). These compounds represent the land-derived diagenetic products of polysaccharides and may be indicative of massive soil erosion (Sephton et al., 2005). The biomarkers of high moretane/hopane ratio commonly occurs in the immature organic matter regardless of the lithology of sediments when accompanied by high maturity stage, it usually indicates terrigenous plant-derived organic matter. These pattern of hopane distribution is called ‘‘coal-type’’ hopane. The high abundance of moretane is most probably related to acidic and oxic conditions in peat or coal enrich sediments.

The C31 hopanes can be formed by the decarboxylation of the C32 hopanoid acids. The C32 Hopanoid acids are formed in the peat deposition environment or Oxic environments and during diagenesis, it becomes the C31 Hopane.

Very high Tm/C30 hopane and Tm/Ts are found in coals or coaly shales both in the immature and mature stage.

Usually Tm (17a(H)-28,29,30-trisnorhopane) is less stable than Ts (18a(H)-28,29,30-trisnorneohopane). If we found High Tm than Ts even in the mature stage it indicates the source input might be peat-forming processes because acidic clay may be the sources of Tm and peat are the sources of acidic clay.

“Coal type” Hopane is called because the ratio of Moretane than Hopane is much higher and this type of hopane anomaly is usual in the coal-forming depositional setting in marine sediments, hence the name.

Hopane/sterane ratio (Sum of C27–C35 hopanes/ Sum of C27–C29 steranes) is usually used to indicates the input of bacteria versus algae (phytoplankton) in sediments. High hopane/sterane ratios usually occur in terrestrial sediments and rocks where bacteria are dominants.

What is Kovats Indices and How to Identify Biomarkers in GCMS (Hopan, Sterane, Coronene, Cadalene, Phenanthrene)

The retention time (RT) is somewhat (several minutes) deviation depending on the condition of the sample and GCMS, so it is a standard only. When actually searching please rely on the interval between peaks and the distance to other peaks of molecules.

By using Retention time index (Kovats indices), it is possible to correct differences in measurement conditions etc., and data that was put in a different laboratory (data being published), data measured at a different time. You can also compare, you can accurately identify organic matter. Chromatography is also effective in searching for organic matter from complex data. By using the following formula, you can see that the positions coming out in all the organic matter come out at the same position regardless of the condition of the sample and GCMS. (By identifying based on the calculated numerical value, organic matter which does not have standard can be used basically in the paper.)

Kovats indices are calculated by

I = 100 (log TX – log TCn) / (log TCn + 1 – log TCn) + 100 n

(100 times the carbon number of the equivalent hypothetical n-alkane having the same retention time as x, where T refers to retention time, x to the component and C n and C n + 1 to the n-alkanes having n and n + 1 carbon atoms, each)

For difficult specimens, it is identified with reference to the value calculated by the above equation.

(If you search by Kovats indices, you will see examples of various organic matter so please refer to it.)

Normal alkane (n-alkane)

Search by m / z;  57. Evenly spaced peaks appear every two minutes. I measure from 14 carbon atoms per 9 minutes to 24 carbon atoms per 27.6 minutes. If you do not know which is which, Pristan and Phytan look for C17 and C18 next to it, or you see the peak of molecular weight in the mass spectrum. C14 = 198, C15 = 212, C16 = 226, C17 = 240, C18 = 254,C19 = 268, C20 = 282, C21 = 296, C22 = 310, C23 = 324,Since C24 = 338, please check whether this value is large respectively.


Search by m / z; 191. When searching for 2α methyl hopane, add 205 at the same time. C30 at about 38 minutes, C30 at about 39 minutes, C31 (2 peaks with optical isomers) at about 40.3 minutes, C32 (about 2 times) at about 41.3 minutes, and every 2 minutes at each minute Peaks are shown by book. Peak will appear so that 2α methylphosphole will almost overlap with this Hopane (slightly late shifts). At the foot of C29 Hopan’s peak seen at m / z 191, I see the peak of 2α methyl fun of C30 seen at m / z 205.


It searches with m / z; 217, but it is easier to compare it with 358, Molecular weight of Cholestane (C27) of 372, Molecular weight of ergostane (C28) of 386, Molecular weight of Stigmastane (C29) of 400 together. A peak appears for each carbon number by 4 optical isomers. The peak of Cholestane comes out around 35 minutes. The former three, three minutes apart and one behind. Peaks appear at the same place in the chromatograms of 358 and 372, so compare them with the chromatogram of 217 side by side. Ergostane will appear around 36.5 minutes. Similarly, the interval between the peaks of 1st and 2nd of the previous 3 somewhat widen, although it is 4 in total, 3 in front, 0.3 in left and 1 in back. Compare the chromatograms of 217 and 372, 386. Stigmastan comes out from 37 to 38 minutes. It is a peak of 4 somewhat hard to find, one before, one with almost 0.3 minutes open and two sticking, another half a minute apart and the last one. Look at the chromatograms of 385 and 400 together.




It is easy to find because it comes out immediately after phenanthrene D body (molecular weight 188) to be put in as a standard around 17 minutes. Look for molecular weight 178. Since standard Phenanthrene D body also has a mass spectrum 178, it may be misunderstood as a standard peak. Please look at the mass spectrum of the peak carefully check that 188 is not contained.

Coronene (Coronene);

PAHs, including coronene, have peaked at half the molecular weight and molecular weight. Since the molecular weight of coronene is 300, we will look for it at 300 and make sure 150 is large on the mass spectrum. The peak appears in my sample around 45 minutes. · Benzo [a] pyrene, benzo [e] pyrene, benzo [fluoroane] (benzo [a, e] pyrene,


We will search for the molecular weight of 252. For benzopyrene, it is most likely that benzo [e] is larger and next to it is benzo [a] pyrene halfway overlapping (only about 0.1 min deviation). Benzo [a] often cannot be determined almost, I have not measured it. It will take about 34.5 minutes. In the mass spectrum, 126, 113 etc. are seen large. Benzofluoran sen is about 33.5 minutes, a peak appears before benzopyrene. Mass spectra similar to benzopyrene, such as 126, 113, can be seen large.


Benzo [g, h, i] perylene (benzo [g, h, i] perylene)

Look for molecular weight 276. It is about 39.5 minutes. Slightly ahead, the peak at about 38.7 minutes is like indene [c, d] perylene, but I have never measured it. In the mass spectrum, 126, 113 etc. are seen large.As far as I know, please contact Mr. Saito about other organic matter of combustion origin.

Aryl isoprenoid;

Aryl isoprenoid will look for it in 133, but 134 will overlap with the size of half of the peak of 133, so I will input it at the same time. A peak appears irregularly with 18 carbon atoms (molecular weight 246) around 18 minutes, carbon number 19 (molecular weight 260) around 19.3 minutes, carbon number 20 (molecular weight 274) around 21.5 minutes. Since it is easy to mix with other peaks on the chromatogram, check the molecular weight peak in the mass spectrum.

Cadalene, Retene:

Cadalene approximately 14 minutes m / z 183 (100%), 198 (around 70%) Reten: Approximately 24 minutes m / z 219 (100%), 234 (About 50%) (There are many similar peaks to note)

Dibenzothiophene spp. (See Asif et al., 2009) Methyl body (M1 & M2 has multiple isomers, so be careful)Mo: m / z 184 (main), 139M1: m / z 198 (main), 165M2: m / z 212 (main), 165


Asif, M., Alexander, R., Fazeelat, T., & Pierce, K. (2009). Geosynthetics of dibenzothiophene and alkyl dibenzothiophenes in crude oils and sediments by carbon catalysis. Organic Geochemistry, 40 (8), 895-901 .


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