Analytica Chimica Acta 446 (2001) 115–120

Chemical knowledge discovery from mass spectral database

I. Isotope distribution and Beynon table
Yizeng Liang a,∗ , Feng Gan b
a College of Chemistry and Chemical Engineering, Institute of Chemometrics and Intelligent Analytical Instruments,
Central South University, Changsha 410083, PR China
b College of Chemistry and Chemical Engineering, Institute of Chemometrics and Chemical Sensing Technology,

Hunan University, Changsha 410082, PR China

Received 7 November 2000; received in revised form 4 April 2001; accepted 11 April 2001

Abstract
A primary approach on data mining (DM) of mass spectral library has been developed in this work. The results obtained
from DM for the first time showed that the ratios of isotope peaks and molecular ion peak obey a logarithm normal distribution.
With the help of statistical inference, the guideline about how to efficiently use Beynon table is also given in order to provide
information for making a decision on the molecular weight or molecular formula in mass spectral analysis from the point of
view of statistics. The work indicates that a wide studying on DM of chemical databases is essential not only for the verification
of the existing knowledge, but also for the discovery of new laws in chemistry. © 2001 Elsevier Science B.V. All rights reserved.
Keywords: Data mining; Beynon table; Statistical inference; Logarithm normal distribution; Chemometrics

1. Introduction chromatographic databases, or a large amount of data

Chemistry is essentially so far a strongly experience-
dependent scientific discipline. Lots of chemists do
lots of chemical experiments and chemical measure-
ment everyday. The major body of knowledge of
chemistry obtained so far is mostly based on chemi-
cal experiments and measurement data, even theoretic
quantum chemistry could explain something in chem-
istry. However, with the development of the chem-
istry and information sciences, one new challenge for
chemists is the spectacular growth of measurement
data that contain a large amount of chemical com-
pound information, such as the spectral databases,
∗ Corresponding author. Tel.: +86-731-882-2841;
fax: +86-731-882-5637.
E-mail address: yzliang@cs.hn.cn (Y. Liang).
on molecular structures and their properties. Could
we directly obtain some useful knowledge from the
rapidly growing volumes of chemical data? Modern
microcomputer that makes the digitized information
easy to capture and fairly inexpensive to store and to
access, which gives us chemists a great opportunity
to extract useful chemical knowledge in databases or
the huge amount of the chemical data. This is also
just the object of new techniques, named knowledge
discovery in databases (KDD) or data mining (DM),
developed quickly in computer science, since the
DM aims to discover something new from the facts
recorded in the databases or huge amount of data col-
lected [1–4]. Recently, Buydens and her colleagues
give such an example for this [5].
As several large-scale databases of mass spectra
are now available, it is possible for us to enlarge and

0003-2670/01/$ – see front matter © 2001 Elsevier Science B.V. All rights reserved.
PII: S 0 0 0 3 - 2 6 7 0 ( 0 1 ) 0 1 0 7 3 - X
116 Y. Liang, F. Gan / Analytica Chimica Acta 446 (2001) 115–120
deepen our knowledge extent in this field. On the other
hand, the high-speed computer and statistical meth-
ods will make the approach easier and fruitful. The
aim of this paper is to show how the DM technique
could work out some useful chemical knowledge in
the databases. First, a comprehensive statistic investi-
gation was conducted, then a primary approach on DM
of mass spectral library has also been developed based
on this information. The rather astonishing results ob-
tained from DM for the first time showed that the ra-
tios of isotope peaks and molecular ion peak obey a
logarithm normal distribution. With the help of statis-
tical inference, the guideline about how to efficiently
use Beynon table is also given in order to provide
information for making a decision on the molecular
weight or molecular formula in mass spectral analysis
from the point of view of statistics. The work indicates
that a broad studying on DM of chemical databases is
essential not only for the verification of the existing
knowledge, but also for the discovery of new rules in
chemistry.
2. Experimental
A mass spectral library was established by trans-
ferring NIST62 mass spectrum library, which is built
in the GCMS-QP5000 of Shimadzu. The data of our
library are stored in the format of binary file and
MATLAB data file. The number of the mass spectra
included in the library is 61999.
The spectra of compounds containing (C, H), (C,
H, O), (C, H, N) or (C, H, O, N) in the NIST62 mass
spectrum library are all collected, respectively. Ratios
of the isotopic peaks with the corresponding molecular
ion peaks are then calculated in this work, but only
the results of (M + 1)/M are presented in this paper.
Thus, an elaborate program was encoded in Matlab to
collect the molecular ion peaks denoted by (M) and the
corresponding isotopic peaks, denoted by (M + 1) and
(M + 2), respectively, and then to calculate the ratios
of (M + 1)/M and/or (M + 2)/M. The true values of
the ratios of the isotopic peaks with the corresponding
molecular ion peaks are obtained by using those listed
in the book of Beynon [6].
The mass spectrum of hexane was measured. The
chemical, say hexane, is of analytical grade. The ex-
periment condition of the GC–MS is the following
Equipment: GC-17A Gas Chromatograph, QP-5000
Mass Spectrometer, Shimadzu.
Detection conditions: An OV-17 capillary column
(30 m × 0.25 mm i.d.) is used. Column temperature is
maintained at 60◦ C for 2 min, programmed from 60
to 270◦ C at a rate of 20◦ C/min. Inlet temperature is
kept at 250◦ C. Helium carrier gas is used at a constant
flow-rate of 1 ml/min.
Mass spectrometer: Electron impact (EI+ ) mass
spectra are recorded at 70 ev ionization energy in
full scan mode in the 40–426 amu mass range with
0.2 s/scan velocity. The ionization source temperature
is set at 230◦ C. Detected spectra are identified by
matching EI+ against the national institute of stan-
dards and technology (NIST) MS database containing
about 62,000 compounds.
All programs are written in MATLAB 5.0 and run
on a PC (CPU 200, RAM128MB).
3. Results and discussion
The molecular ion peak, denoted by (M) in this pa-
per, is very important in mass spectral analysis, since
with the help of the molecular ion peak, people could
easily obtain some information on molecular weight as
well as molecular formula. Beynon table is a common
tool for checking the molecular ion peak and molec-
ular formula in mass spectral analysis, in which the
ratios of (M + 1)/M and/or (M + 2)/M are given as
constants according to the isotopic abundance of each
element in nature. Thus, one could identify if a peak
is really a molecular ion peak by comparing the calcu-
lated abundance ratio of (M + 1)/M and/or (M + 2)/M
with the one listed in the Beynon table. Thus, most
of the text books on mass spectral analysis will be at-
tached a Beynon table for the convenience of users
usage [7,8]. However, when we worked with the table,
we found that the consistent rate between the measured
abundance ratio of (M + 1)/M and the value listed in
Beynon table is rather lower. (Table 1). Is there some-
thing wrong for the Beynon table or something hidden
in the facts?
With the help of the NIST62 mass spectral database,
in which 62199 mass spectra were collected, a broad
survey of the molecular ion peaks and their corre-
sponding isotopic peaks, say (M + 1) and (M + 2)
peaks, was conducted. Totally, 18170 mass spectra, in
 Y. Liang, F. Gan / Analytica Chimica Acta 446 (2001) 115–120 117

Table 1
Investigation results for consistent rate between the measured abundance ratios of isotopic peaks and molecular peaks with the ones listed
in Beynon table
Range of Number of Com. Part. con. Devia. (+10 Devia.(−10 Devia. Devia. Total rate
molecular samples con. with.b to +50%)c to −50%) (>+50%) (<−50%) of consis.d
weight with.a
0–50 35 1 14 6 8 3 3 42.86
51–70 130 5 49 22 32 19 3 41.54
71–90 385 24 103 71 67 91 29 32.99
91–110 756 58 277 109 145 118 49 44.31
111–130 1388 80 456 274 275 225 78 38.62
131–150 1979 110 808 348 398 201 114 46.39
151–170 1772 130 744 344 316 148 90 49.32
171–190 2244 110 900 402 450 228 154 45.01
191–210 1740 136 749 370 350 135 100 50.86
211–230 1361 119 586 213 271 106 66 51.80
231–250 1164 135 509 178 205 80 57 55.33
a Com. con. with.: completely consistence with the ones listed in Beynon table (deviation ≤ 5%).
b Part. con. with.: partially consistence with the ones listed in Beynon table (5% < deviation ≤ 10%).
c Devia. (+10 to +50%): deviations between the range of +10 to +50%.
d Total rate of consis.: total rate of consistence, including the ones of deviations within ±10%.

which 1681 molecular formulae are included, were in-
vestigated. Except for 5216 mass spectra neither with-
out molecular ion peaks or without (M + 1) peaks, the
abundance ratios of (M + 1)/M and/or (M + 2)/M of
12954 mass spectra are calculated. For the compounds
with the molecular formulae CW HX NY OZ , the calcu-
lation formula for the abundance ratio of M/(M + 1)
listed in Beynon table can be as follows
Ratio(M+1), Beynon
= (1.08W + 0.016X + 0.38Y + 0.04Z)
where Ratio(M+1),Beynon denotes the abundance ratio
of (M + 1)/M listed in Beynon table. The deviation
of measured ratio of M/(M + 1) and the value listed
in the Beynon table can then be estimated using the
following equation
Deviation %
Ratio(M+1), measured − Ratio(M+1), Beynon
= 100 ×
Ratio(M+1), Beynon
(2)
the results obtained are shown in Table 1. From
the table, one can easily see that simply using the
Beynon table to confirm the molecular ion peak
(or molecular weight) as well as molecular formula
might be misleading, since the complete consis-
tent rate with the values in the Beynon table is
only around 5–10% (column 2 and column 3 in
Table 1). Notice that here we say that the ratios cal-
culated are completely consistence with the one list
in the Beynon table if and only if their deviations are
within ±(5%) for both (M + 1) peaks and (M + 2)
peaks. The total consistent rate only for (M + 1)
peaks is around 50% (last column in Table 1). Almost
half the deviations fall into the range of ±(10–50%),
(1) (column 5 and column 6 in Table 1), and some even
are beyond the range from −50 to +50%. The results
seem to suggest that the measured ratios of (M + 1)/M
may obey some statistical distribution.
In order to confirm this assumption, a comprehen-
sive investigation over the whole database of mass
spectra was then conducted. The molecules contain-
ing (C, H), (C, H, O), (C, H, N) or (C, H, O, N) were
all investigated. The total number of the compounds
in the database containing only elements carbon and
hydrogen is 4463. The results are shown in Fig. 1.
From this plot, one can see that the distribution of
the abundance ratios of isotopic peaks with molecular
peaks, say (M + 1)/M, looks like normal distribution
(top part in Fig. 1) with some tailing. However, if
we use the normal probability plot to check if it is
an approximately normal distribution, the answer is
118 Y. Liang, F. Gan / Analytica Chimica Acta 446 (2001) 115–120

Fig. 1. Statistical results for compounds embracing carbon and
hydrogen. Top part: the deviation distribution diagram of the mea-
sured abundance ratios of (M + 1)/M compared to the ones in
Beynon table; low left part: the normal probability plot of the
distribution; low right part: the normal probability plot of the dis-
tribution after logarithm transformation.
Fig. 2. Statistical results for compounds embracing carbon, hy-
drogen and nitrogen. Top part: the deviation distribution diagram
of the measured abundance ratios of (M + 1)/M compared to the
ones in Beynon table; low left part: the normal probability plot of
the distribution; low right part: the normal probability plot of the
distribution after logarithm transformation.

negative. The result is shown in Fig. 1 (plot in low left It is worthy noting that the ability of any method
part in Fig. 1). The observations can not be expressed to work with is strongly determined by the repro-
by a straight line in the normal probability plot. What ducibility of the intensities (abundance) in mass spec-
kind distribution will the abundance ratios of isotopic tra. It was found that the mass spectral intensities have
peaks with molecular peaks obey? Then, the loga- strong heteroscedastic noise [9]. Thus, the influence
rithm normal distribution was tried. The results are from the heteroscedastic noise on the intensities of
also shown in Fig. 1 (plot in lower right part in Fig. 1).
The results clearly show that they approximately
obey the logarithm normal distribution. In order to
further confirm this result, we continue to investigate
the compounds containing element carbon, hydrogen
and nitrogen (C, H, N) with the total number of 4310
molecules, the compounds containing element carbon,
hydrogen and oxygen (C, H, O) with the total number
of 9833 molecules, and the compounds containing
element carbon, hydrogen, nitrogen and oxygen (C,
H, O, N) with the total number of 10519 molecules.
The results are shown in Figs. 2–4, respectively. From
these figures, one can see that the abundance ratios
of isotopic peaks with molecular peaks obey really
the logarithm normal distribution. Especially, the re-
sults shown in Figs. 3 and 4 demonstrate the perfect
agreements between the assumption and facts. The Fig. 3. Statistical result for compounds embracing carbon, hydro-
gen and oxygen. Top part: the deviation distribution diagram of
reason for this might lie in that the total numbers of
the measured abundance ratios of (M + 1)/M compared to the
the compounds of (C, H, O) and (C, H, O, N) are ones in Beynon table; low left part: the normal probability plot of
much larger than the numbers of compounds of (C, the distribution; low right part: the normal probability plot of the
H) and (C, H, N), say 9833 and 10,519, respectively. distribution after logarithm transformation.
 Y. Liang, F. Gan / Analytica Chimica Acta 446 (2001) 115–120
Fig. 4. Statistical results for compounds embracing carbon, hy-
drogen, nitrogen and oxygen. Top part: the deviation distribution
diagram of the measured abundance ratios of (M + 1)/M compared
to the ones in Beynon table; low left part: the normal probability
plot of the distribution; low right part: the normal probability plot
of the distribution after logarithm transformation.
mass spectra should be taken into account when one
uses ratio of M/(M + 1) to decide whether a m/e peak
is a molecular peak with the help of the Beynon ta-
ble. Similarly, Grotch found several decades ago that
abundance values of ion fragments measured by mass
spectroscopy closely follow a logarithm normal distri-
bution [10]. This fact is consistent with the facts we
found in this work. In order to confirm this conclusion,
we further conducted some experiments on measuring
some known compounds, i.e. hexane, on GC–MS to
check the idea. The result is shown in Fig. 5. From this
plot, one can see that the logarithm normal distribu-
tion can also be seen even for one compound. This fact
shows clearly that one can not simply use the ratio of
(M + 1)/M as a constant as commonly used in chem-
istry. One has to consider it is really a random variable
obeying a logarithm normal distribution. Thus, in or-
der to arrive at some conclusion, the statistic inference
technique is necessary to conduct.
4. Conclusion
The results obtained in this work from DM shows
for the first time that the abundance ratios of isotope
peaks and molecular ion peak obey a logarithm normal
119
Fig. 5. Statistical results for compound hexane measured on
GC–MS. Top part: the deviation distribution diagram of the mea-
sured abundance ratios of (M+1)/M compared to the ones in
Beynon table; low left part: the normal probability plot of the
distribution; low right part: the normal probability plot of the dis-
tribution after logarithm transformation.
distribution. This suggests that DM based on efficient
computer-calculation on large databases is quite nec-
essary, since DM is useful not only for the verification
of the existing knowledge, but also for the discovery
of new knowledge in chemistry. On the other hand, the
databases of large quantity and high quality spectra,
including infrared, mass, NMR and UV-visible spec-
tra, are available in recent years. How to efficiently
use the chemical information accumulated from a long
history of chemical researches will be a new challenge
for the chemists. We believe in that a comprehensive
DM upon mass spectral library will give a chance to
develop a new kind of expert system which must be
more strong and effective.
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