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DEVELOPMENTS IN FT-ICR MS INSTRUMENTATION,

IONIZATION TECHNIQUES, AND DATA INTERPRETATION


METHODS FOR PETROLEOMICS
Yunju Cho,1 Arif Ahmed,1 Annana Islam,1 and Sunghwan Kim1,2*
1

Department of Chemistry, Kyungpook National University, Daegu 702-701,


Korea
2
Green-Nano Materials Research Center, Daegu 702-701, Korea
Received 24 June 2012; revised 25 November 2013; accepted 26 March 2014
Published online 18 June 2014 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/mas.21438

Because of the increasing importance of heavy and unconventional crude oil as an energy source, there is a growing need
for petroleomics: the pursuit of more complete and detailed
knowledge of the chemical compositions of crude oil. Crude oil
has an extremely complex nature; hence, techniques with ultrahigh resolving capabilities, such as Fourier transform ion
cyclotron resonance mass spectrometry (FT-ICR MS), are
necessary. FT-ICR MS has been successfully applied to the study
of heavy and unconventional crude oils such as bitumen and
shale oil. However, the analysis of crude oil with FT-ICR MS is
not trivial, and it has pushed analysis to the limits of instrumental and methodological capabilities. For example, high-resolution mass spectra of crude oils may contain over 100,000 peaks
that require interpretation. To visualize large data sets more
effectively, data processing methods such as Kendrick mass
defect analysis and statistical analyses have been developed.
The successful application of FT-ICR MS to the study of
crude oil has been critically dependent on key developments in
FT-ICR MS instrumentation and data processing methods.
This review offers an introduction to the basic principles, FTICR MS instrumentation development, ionization techniques,
and data interpretation methods for petroleomics and is
intended for readers having no prior experience in this field
of study. # 2014 Wiley Periodicals, Inc. Mass Spec Rev
34:248263, 2015
Keywords: mass spectrometry; nano; laser desorption; time of
flight; petroleum

I. INTRODUCTION
Energy has played an important role in the development of
human society by enabling change or adaptation to the natural
environment. Energy is even more important for modern
industrialized society due to its contribution to food production,
heating, construction, and transportation. It has been estimated
that approximately 10 times more energy per person is
consumed in the modern industrialized society than in the

Contract grant sponsor: National Research Foundation of Korea;


Contract grant number: NRF-2012R1A2A2A01044853; Contract
grant sponsor: Ministry of Oceans and Fisheries of Korea; Contract
grant number: PM57431.

Correspondence to: S. Kim, Green-Nano Materials Research Center,
Daegu 702-701, Korea. E-mail: sunghwank@knu.ac.kr

Mass Spectrometry Reviews 2015, 34, 248263


# 2014 by Wiley Periodicals, Inc.

agricultural society. The enormous amount of energy used to


maintain human society contributes to problems such as
pollution and global warming. Ironically, one of the problems is
related to energy itself: the forthcoming shortage of energy
resources. Crude oil has been one of the most heavily used
energy resources, and it is well-known that the supplies of crude
oil are limited. Therefore, alternative energy sources such as
biofuels have gained a lot of attention, but it will take decades
for our energy and industrial infrastructures to thoroughly adapt
to new energy sources (Barrow, 2010).
Another more immediate way to cope with the problem is
to increase the efficiency of processing crude oils into
economically valuable light fractions such as naphtha. This is
increasingly important nowadays because the worlds crude oil
deposit has become heavier (Headley, Peru, & Barrow, 2009).
Heavy crude oils tend to yield higher portions of petroleum
residues that are less economically valuable than lighter
fractions. Detailed characterization of the heavy component is
essential to understand the underlying chemistry of petroleum
processing and improve the process. Gas chromatography (GC)
and gas chromatography mass spectrometry (GC-MS) have
been successfully used for the detailed characterization of crude
oils (Mahe et al., 2011; Dutta, Bhattacharya, & Raju, 2013).
However, these techniques are limited in their characterization
of polar and/or heavy components (molecular weight > 400
Da). Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled to various ionization sources has
been widely used to study such components (Marshall &
Rodgers, 2008). By applying FT-ICR MS, knowledge of crude
oil has been extended to compounds up to approximately
800 Da having polar functional groups (Rodgers et al., 2000;
Hughey, Rodgers, & Marshall, 2002; Xian, Hendrickson, &
Marshall, 2012). For example, electrospray ionization (ESI)
coupled to FT-ICR MS is a powerful tool to study nitrogen
containing and oxygenated compounds. Thousands of crude oil
compounds have been identified by this technique (Marshall &
Rodgers, 2004).
The success of FT-ICR MS for the study of crude oil has
been possible thanks to key advances in FT-ICR MS instrumentation, ionization techniques, and data processing methods. For
example, it would have been much more difficult to process and
visualize complex high-resolution mass spectra of crude oils
without the development of the Kendrick mass defect (KMD)
and van Krevelen analytical methods (Hsu, Qian, & Chen, 1992;
Hughey et al., 2001b; Kim, Kramer, & Hatcher, 2003). Additional instrumental and methodological developments are still

METHODS FOR PETROLEOMICS

needed to overcome current challenges in the analysis of highresolution mass spectra of crude oils. It is not an overstatement
to say that deepening our knowledge of petroleum compounds is
critically dependent on advances in FT-ICR MS instrumentation
and data processing methods. Therefore, the objective of this
article is to provide a review of developments related to
the analysis of crude oils. The topics covered include FT-ICR
MS instrumentation, the ionization method, calibration and
calculation of elemental formulae, method development for
data interpretation, and the combination of FT-ICR MS with
separation techniques.

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motions are small and do not induce enough signal for detection.
Therefore, the ions are excited to have a larger radius of cyclic
motion for detection by use of RF potential. During the
excitation step, the frequency of the reduced cyclic motion does
not change.
Recording of image current is performed after excitation
step with time delay is given. The recording is done over time,
and the obtained signal is called the time domain signal. The
time domain signal is then converted to the frequency domain
spectrum by Fourier transformation. The frequency domain
spectrum is converted to the mass spectrum by use of calibration
equations (Zhang et al., 2005).

II. PRINCIPLES OF FT-ICR MS


B. Resolution of FT-ICR MS Spectra

A. Cyclotron Motion of Ions in the Presence of a


Magnetic Field
To effectively use FT-ICR MS, it helps to understand the basic
principles of the technique. The detailed principles can be found
in previously published review articles or books (Marshall, 1985,
2000; Marshall & Verdun, 1990; Marshall, Hendrickson, &
Jackson, 1998). In this article, the basic principles of FT-ICR
MS are briefly described to assist researchers who use the
instrument for crude oil analysis. With FT-ICR MS, the m/z
values of ions are measured by observing the frequency of
cyclotron rotation of ions subjected to a high magnetic field.
Cyclotron rotation is caused by the Lorentz force exerted on an
ion of mass m and charge q moving in a static magnetic field B.
If there is no extra electric field applied to the ion, the ions
cyclotron angular frequency, vc (in rad/sec), is described by
the following equation (Marshall & Verdun, 1990; Marshall,
Hendrickson, & Jackson, 1998):
vc

qB
m

In practice, ions have to be kept in a defined space (e.g.,


an ICR cell) for frequency measurement, and hence applying
an extra electric field to the ions is unavoidable. The ions are
confined axially (the direction parallel to the magnetic field,
B) by a trapping electric field and radially (direction perpendicular to B) by the Lorentz force. In a typical closedcylindrically shaped ICR cell, the ions are injected into the
cell along the axial direction. When a trapping potential is
applied to trap the ions, the motion of the ions can no longer be
described according to Equation (1). Under the quadrupolar
potential, the motion of the ions is a combination of three
modes. The first motion is an axial oscillation parallel to
B with frequency vz, the second motion is cyclotron motion
with reduced frequency v, and the third is rotational
motion perpendicular to B having the magnetron frequency
v. Cyclotron motion with reduced frequency is what we
measure for mass analysis, and the equation describing the
motion is as follows (Marshall & Verdun, 1990; Marshall,
Hendrickson, & Jackson, 1998):
r
v 2 v2
vc
c
v

2
 z
2
2
2
The cyclic motions of confined ions are typically detected
by measuring the image current induced by ions in the detection
plates of the ICR trap. However, initially, the radii of cyclic
Mass Spectrometry Reviews DOI 10.1002/mas

The resolution of FT-ICR MS is often described by the fullwidth-at-half-maximum, (m/(Dm50)) (FWHM). The resolving
power of an FT-ICR MS signal with a molecule of mass-tocharge ratio m/z is described by the following equation (Marshall
& Verdun, 1990; Marshall, Hendrickson, & Jackson, 1998):
m
CBT

Dm50
m=z

where T is the data acquisition time for a given time domain


signal, B is the strength of the magnetic field, and C is a constant.
Therefore, recording the time domain signal for a longer period
of time (i.e., for larger T) can improve mass resolution. It is
important to note that resolving power for a given FT-ICR
system is not a static value, but it can be changed depending on
experimental parameters. Therefore, when FT-ICR MS spectra
are interpreted, experimental parameters used to obtain the data
have to be considered.
Typically, optimum length of time domain signal is
determined by considering stability of coherent ions motions
in the ICR cell. When they are stable, a slowly exponentially
decaying time domain signal can be obtained. In that case,
maximum length of recording time allowed under given
experimental parameters can be used. However, if the time
domain signal dies off quickly, acquiring data for extended
period of time will deteriorate signal to noise ratio of data.
Therefore, acquire data for an extended period time is not
helpful in that case.
The typical experimental parameters determining length of
recorded time domain signal are data size and sampling
frequency. The data size is basically indication of number of data
points taken during the data acquisition. The more data points are
taken the larger the data size is. The maximum data size (and
hence the maximum data point) is determined by the size of the
memory located in the analog-to-digital converter (ADC) board.
User can choose the data size before data acquisition starts. The
sampling frequency is the rate at which data points are sampled
and memory is filled. The higher the sampling frequency, the
faster the memory is filled up. In summary, a longer signal can be
obtained by a combination of smaller sampling frequency, larger
data size, and more stable ion motions.
The sampling frequency, based on the Nyquist theorem
(Nyquist, 1924), is also determined by the low mass cut-off
values of mass spectra (Marshall & Verdun, 1990; Marshall,
Hendrickson, & Jackson, 1998). According to the Nyquist
theorem, sampling frequency has to be at least twice of the
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CHO ET AL.

highest frequency observed in spectra. In FT-ICR MS data,


compounds with lowest m/z have the highest frequency.

III. INSTRUMENTAL DEVELOPMENTS


A. ICR Traps
One factor that contributes to the increased stability of
coherent ICR motion is maintaining an ideal quadrupolar
electric field inside the ICR trap. When the electric field inside
an ICR trap deviates from the ideal quadrupolar electrostatic
field, the trapped ions become radially unstable, causing radial
ejection of ions. Ultimately, a non-ideal electrostatic field will
result in quicker damping of the time domain signal (Marshall
& Verdun, 1990; Marshall, Hendrickson, & Jackson, 1998).
It was reported that injection of electrons or reducing the
trapping voltage at the detection step improved the stability of
trapped ions (Kaiser & Bruce, 2005; Kim et al., 2007). These
studies clearly showed that extra electric field was necessary
to compensate for the imperfection of the electric field.
Therefore, a number of studies have been devoted to improving the design of conventional ICR traps by making the
electric field closer to ideal.
One of the trap designs combined the features of the infinity
cell, compensated cell, and capacitively coupled open cylindrical cell (Kim et al., 2008). Since this cell has more degrees of
freedom to control the electric field, a more ideal electric field is
obtained. In another design, more ring electrodes were added to
a conventional capacity-coupled open cell design to add more
degrees of freedom (Tolmachev et al., 2008). A cell with this
design has been built and incorporated into an FT-ICR MS
instrument (Kaiser et al., 2011). Crude oil spectra with a
resolving power of 800,000 at m/z 500 and 124 ppb root mean
square (RMS) error could be obtained with the 9.4 T FT-ICR
MS (Kaiser et al., 2011). Nikolaev et al. (2011) reported a new
FT-ICR cell with dynamic harmonization. Greater than
20,000,000 resolving power at m/z 609 was achieved with the
cell installed in a 7 T magnetic field. Since this cell is effective
for ions rotating at larger radii, it is expected that it would
be effective in complex mixture analysis. It is because space
charge effect will be less severe for ions rotating with larger
radii.

2010; Hur et al., 2010a,b; Kim & Kim, 2010; Cho, Kim, &
Kim, 2011; Kim et al., 2011; Cho et al., 2012c; Jin, Kim, &
Birdwell, 2012). Currently, a 21 T FT-ICR MS is being
developed in the National High Magnetic Field Laboratory at
Florida State University and Pacific Northwest Laboratory
(Marshall et al., 2012).

C. Data Acquisition System and Automation


The data acquisition system is a key component of an FT-ICR
instrument. It enables control of ion movement, excitation and
detection events, and transfer of data from the acquisition board
to the computer. For example, a series of analog and on/off
digital signals that constitute an experimental pulse sequence
are applied to ion lenses and multipoles through the data
acquisition system. A data acquisition system optimized for
complex mixture analysis has been developed and used for
petroleum research (Blakney, Hendrickson, & Marshall, 2011).
This flexible system includes 17 channels of analog voltage, 18
TTL triggers, and a 6-channel high-power dc voltage amplifier
(Kim et al., 2007).
The data acquisition system has been used for automated
analysis of crude oils (Kim et al., 2009). Automation is
important because typical crude oil analysis by FT-ICR MS
takes a long time. This is because detection by FT-ICR MS is
typically limited to 1,000,000 ions at a time, but a single
petroleum FT-ICR mass spectrum can contain up to 30,000
compounds. At least 100 ions of the same kind are required
for detection. Thus, the number of ions detected for each
compound is small, and summing 100200 time domain signals
is often needed to improve the S/N ratio and dynamic range. A
longer time domain signal is also beneficial for improved
resolving power. The total data acquisition time for a single
crude oil sample can take 2060 min. To circumvent this
problem, an automated chip-based micro-ESI system has been
used for crude oil analysis (Kim et al., 2009). Prevention of
solvent evaporation was an important part of the development
of the system. Because volatile solvents such as toluene are
used for petroleum analysis, it is difficult to keep the sample
intact on the sample plate of an automated ESI system for an
extended time period. Aluminum foil-sealed 96-well glass
plates and compression plates made of aluminum were used to
minimize evaporation.

B. High-Field FT-ICR MS
The ultimate way to increase the resolving power of FT-ICR MS
is to increase the strength of the magnetic field. A stronger
magnetic field also improves other critical performance parameters such as mass accuracy, speed of analysis, and dynamic
range. The need for higher resolving power is obvious for the
study of petroleum because there are many elemental compositions that cannot be fully resolved even with the highest field
magnet currently available (Hsu, 2012). Therefore, continuous
efforts have been made to develop FT-ICR MS instruments
having higher magnetic fields to study crude oils. Magnetic field
strengths of 9.4, 12, 14.5, and 15 T have been mostly used to
study petroleum samples (Senko et al., 1996; Schaub et al.,
2008; Kim & Kim, 2010; Gaspar et al., 2012a). A 15 T
instrument was installed at the Korean Basic Science Institute
located in Ochang, Korea in 2007. This instrument has greatly
contributed to the study of crude oil in Korea (Bae et al.,

250

D. Absorption Mode Spectra


Another important area of development uses absorption mode
instead of magnitude mode spectra. When a time domain ICR
signal is processed by Fourier transformation, two frequency
domain spectra result, that is, absorption (A(W)) and dispersion
(D(W)) spectra. Mathematically, A(W) corresponds to the real
part and D(W) to the imaginary part of the frequency domain
spectra. The magnitude mode spectra (M(W)) are calculated as
the root sum square of A(W) and D(W). Normally, M(W) is
used instead of A(W) in FT-ICR MS analyses because of the
phase problem. If ions start their cyclotron motions simultaneously (i.e., they have the same phase), A(W) can be calculated
from the obtained signal. However, in reality, ions do not start
simultaneously because of detection delay, chirp excitation, and
other factors. Therefore, it has been very difficult to calculate
A(W) from obtained signals.
Mass Spectrometry Reviews DOI 10.1002/mas

METHODS FOR PETROLEOMICS

However, in theory, using the peak width from the A(W)


spectrum is better than using the magnitude mode spectrum by
a factor of Marshall, Hendrickson, and Jackson (1998).
Therefore, it is advantageous to obtain and use A(W) instead of
M(W). The phase correction used to calculate absorption mode
spectra has been achieved by simultaneous excitation and
detection (Beu et al., 2004). However, this method required
complete nulling of the excitation signal induced in the
detection plate, which was difficult to achieve. Instead, phasing
parameters for given experimental parameters can be experimentally determined and applied to phase spectra (Xian et al.,
2010). In another approach, experimental data were mathematically treated to obtain a phase shift function (Qi et al., 2011a,b,
2012). The calculation was done by quadratic least-squares
fitting of the phase shift function. Figure 1 shows the enhancement of resolution achieved by this approach (Qi et al., 2012;
Cho et al., 2014). It has also been shown that the S/N ratio and
mass accuracy can be improved by at least 1.4-fold. Overall,
obtaining and using absorption mode spectra appears very
promising to increase the resolving power of existing FT-ICR
MS instruments for petroleum analyses without significant
additional cost.

FIGURE 1. Close-up of two narrow m/z windows in the oil spectrum, in


both magnitude and absorption-mode [(a) m/z 750.41750.82, (b) m/z
751.41751.83]. Refer to the original article about peak assignment.
Reprinted with permission from Qi et al. (2012). Copyright (2012) American
Chemical Society.

Mass Spectrometry Reviews DOI 10.1002/mas

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IV. STUDY OF IONIZATION METHODS


There is no universal ionization technique that can ionize all the
compounds in crude oils simultaneously. Each ionization
technique has its own advantages for specific chemical structures or functionalities (Panda, Andersson, & Schrader, 2009).
The selectivity of an ionization technique can be important
when a certain group of compounds is targeted. However, when
a broad overview of the compounds existing in a crude oil is
needed, such selectivity can be problematic. Therefore, it is very
important to understand the nature of the various ionization
techniques and to be able to apply each one appropriately to
study complex and heterogeneous mixtures such as crude oils.

A. Electrospray Ionization and Desorption Ionization


Electrospray ionization (ESI) is typically achieved by applying
a high voltage to crude oil dissolved in a mixture of toluene and
methanol. A few microliters of formic acid can be added to the
solution in the () mode and ammonium hydroxide in the ()
mode to improve the ionization efficiency. The direct infusion
method is typically used for ESI, and the optimum flow rate
depends on the design of the ESI source. ESI is efficient at
ionizing compounds having polar functional groups containing
nitrogen and oxygen atoms, but it is not efficient for molecules
lacking nitrogen or oxygen atoms. To overcome this limitation,
chemical derivatizations have been combined with ESI to detect
broader classes of molecules. ESI is insensitive towards sulfurcontaining compounds and so methylation of sulfur compounds
has been used to increase the detection sensitivity (Muller,
Andersson, & Schrader, 2005; Panda, Schrader, & Andersson,
2008). Liu et al. (2010b) oxidized sulfides in petroleum and
identified them using ()-ESI FT-ICR MS (Liu et al., 2010b).
ESI is one of the major ionization techniques used to study crude
oils and there have been a number of publications using this
technique for oil analyses (Zhan & Fenn, 2000; Hughey
et al., 2001a; Qian et al., 2001a,b; Hughey, Rodgers, &
Marshall, 2002; Barrow et al., 2003, 2009; Hemmingsen
et al., 2006; Klein et al., 2006; Mullins et al., 2006; Stanford
et al., 2006, 2007a,b; Teravainen et al., 2006; Headley et al.,
2007; Panda et al., 2007; Schaub et al., 2007; Mapolelo
et al., 2008; Miyabayashi et al., 2008; Smith et al., 2008a,b; Da
Campo et al., 2009; Juyal et al., 2009, 2010; Shi et al., 2009,
2010a,b; Liu et al., 2010b; Zhang et al., 2010, 2011; Zhu et al.,
2010; Li et al., 2011; Chen et al., 2012; Gaspar et al., 2012b; Jin,
Kim, & Birdwell, 2012).
Electrospray ionization (ESI) has also been combined with
desorption ionization and applied to crude oil analysis (Eckert
et al., 2011). Different classes of compounds can be observed
depending on their solubilities in different solvents. For example, water-soluble compounds were observed when methanol/
water was electrosprayed onto oil drops loaded on a glass plate.
In another example, ESI was combined with sonic spray and
desorption ionization, referred to as easy ambient sonic-spray
ionization mass spectrometry (EASI) (Corilo et al., 2010). EASI
was successfully applied to a single droplet of crude oil placed
on an inert surface; EASI spectra were similar to those from a
commercial nanochip-based ESI system (Corilo et al., 2010).
Zhou et al. (2012) used ruthenium-ion-catalyzed oxidation
(RICO) and lithium aluminum hydride (LiAlH4) reduction
reactions to convert branched and cyclic alkanes to monohydric

251

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CHO ET AL.

alcohols (O1) and measured them with ()-ESI FT-ICR MS


(Zhou et al., 2012).

B. Atmospheric Pressure Photoionization and


Chemical Ionization
Atmospheric pressure photoionization (APPI) is performed by
exposing analytes to 10 eV photons emitted from a UV lamp.
Since this ionization technique relies on absorption of photons,
and an aromatic group is a good chromophore for absorbing UV,
APPI is more sensitive towards aromatic compounds. Sulfurcontaining compounds, especially those with thiophene structures, are also easily ionized (Panda, Andersson, & Schrader,
2009). Chemical reaction followed by photon absorption is also
an important process for APPI (Ahmed et al., 2011). Therefore,
both molecular (M) and protonated ([M H]) ions are
generated in ()-mode APPI. Deprotonated ions are mainly
generated in ()-mode APPI. APPI has been used extensively
for the study of crude oil (Purcell et al., 2006, 2007a,b,c, 2010;
Qian et al., 2008b, 2010; Haapala et al., 2009; Bae et al., 2010;
Barrow et al., 2010; DAndrilli et al., 2010; Podgorski et al.,
2010; Cho et al., 2012c; Cho, Ahmed, & Kim, 2013).
Atmospheric pressure chemical ionization (APCI) is a
technique in which analytes and solvent mixtures are sprayed
into a region where corona discharge is maintained by applying
a high voltage to a sharp needle (Smaniotto et al., 2008; Borton
et al., 2010; Kim et al., 2010; Gaspar et al., 2012b). It has been
reported that detection using APPI allowed a broader overview
of crude oil compounds than ESI or APCI (Panda, Andersson,
& Schrader, 2009).

C. Laser Desorption Ionization and Atmospheric


Pressure Photoionization
Laser desorption ionization (LDI) coupled to high-resolution
mass spectrometry has been used to study crude oils (Cho et al.,
2012b,d). Class distribution plots observed from the same
sample but with ()-mode APPI and ()- and ()-mode LDI
FT-ICR MS are presented in Figure 2. Nitrogen-containing

compounds were more abundant in the spectra obtained by ()LDI than with ()-APPI. It was concluded that the lower
ionization energy of nitrogen-containing compounds contributed to stronger signals. The spectrum obtained using ()-LDI
contained abundant Ox-class compounds. Non-aromatic (presumably naphthenic acids) and aromatic Ox-class compounds
can be detected simultaneously using ()-LDI. Therefore, it has
been suggested that ()-LDI is suitable for studying naphthenic
acids (Cho et al., 2012d).
Atmospheric pressure laser ionization (APLI) is a technique in which laser radiation is used for ionization (Schrader
et al., 2008; Panda et al., 2011; Gaspar et al., 2012a). APLI
coupled to FT-ICR MS has been applied to study crude oil
samples (Schrader et al., 2008; Panda et al., 2011; Gaspar
et al., 2012a). The basic design of APLI is similar to that of
APPI except that a UV laser is used instead of a krypton lamp.
Typically, 45 eV laser photons are used for the ionization;
multi-photon absorption is the major ionization mechanism.
APPI and APLI cover similar classes of compounds in crude oils
(Panda, Andersson, & Schrader, 2009). APLI has been combined with chip-ESI as a multimode ionization source for crude
oil analysis (Schmitt-Kopplin et al., 2008).

D. Field Desorption Ionization, Electron Ionization,


and Laser-Induced Acoustic Desorption Ionization
The techniques described above are efficient at ionizing polar
constituents but are not effective towards non-polar compounds
such as aliphatic hydrocarbons. Non-polar compounds are
major components of crude oil, and hence it is important to
characterize them. Field desorption ionization (FD) (Schaub
et al., 2003, 2005a,b; Smith et al., 2008a,c) and electron
ionization (EI) (Fu et al., 2006a,b) have been coupled to FTICR MS. Both techniques have been used to study processed
oils.
Laser-induced acoustic desorption (LIAD)-(EI/CI)/FT-ICR
MS has been applied to crude oil and asphaltene (Crawford
et al., 2005; Duan et al., 2008; Pinkston et al., 2009). In LIAD,
the sample is loaded onto a thin metal foil and the backside of
the foil is irradiated with a laser pulse. The acoustic waves
generated by the laser pulse results in desorption of the analytes.
The desorbed analytes are ionized in vacuum by either EI or CI.
Studies have shown that LIAD can successfully vaporize a
variety of compounds. However, carrying out the ionization
under vacuum severely limits the throughput of analyses.
Hence, atmospheric pressure LIAD-CI (AP/LIAD-CI) has been
developed (Nyadong et al., 2011).

V. COMBINING HIGH-RESOLUTION MASS


SPECTROMETRY WITH SEPARATION TECHNIQUES
A. Combination With the Saturates, Aromatics,
Resins, and Asphaltenes Chromatographic Method

FIGURE 2. Comparison of class distributions calculated from spectra


obtained with LDI and APPI FT-ICR MS in positive-ion mode and LDI FTICR MS in negative-ion mode.

252

All the ionization methods developed so far suffer from a matrix


effect to some degree. The matrix effect can limit the number of
compounds observed by mass spectrometry (Cech & Enke,
2000; King et al., 2000; Trufelli et al., 2011). Additionally,
ionization of compounds having low abundances and/or ionization efficiencies can be suppressed. To reduce the matrix effect
and/or ionization suppression, chromatographic separation
Mass Spectrometry Reviews DOI 10.1002/mas

METHODS FOR PETROLEOMICS

techniques such as liquid chromatography and gel electrophoresis have been used along with MS analysis.
The saturates, aromatics, resins, and asphaltenes (SARA)
method is a chromatographic technique that has been widely
used to fractionate crude oil compounds based on their
chemical compositions. SARA and FT-ICR MS with various
ionization sources have been combined to study crude oils at
the molecular level. The spectra obtained by ()-mode ESI FTICR MS analyses of unfractionated crude oil and its aromatic
fraction were quite similar. Therefore, it was concluded that
isolation of the polar aromatic fraction is not necessary to
characterize its chemical composition (Klein et al., 2006).
Sulfur compounds in SARA fractions were investigated using
()-ESI FT-ICR MS and sulfur methylation (Liu et al., 2010a).
()-ESI FT-ICR MS analysis was applied to SARA fractions
for neutral nitrogen compounds (Shi et al., 2010a; Zhang
et al., 2010).
Figure 3 compares the number of peaks and class distribution observed by APPI FT-ICR MS with and without SARA
fractionation (Cho et al., 2012c). The total number of observed
peaks was significantly greater using SARA combined with
APPI-FT-ICR MS than by direct analysis of the unfractionated
crude oil. The increase was more significant for minor components, such as the N1O1, N1O1S1, and N2 classes, than for the
major classes, such as S1 and S2. The reason behind the increase
in number of peaks was attributed to a reduction of matrix
effects and/or ionization suppression (Cho et al., 2012c). APLI
FT-ICR MS combined with SARA fractionation also significantly increased the number of observed peaks (Gaspar et al.,
2012a).

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Relatively minor components, such as vanadyl and nickel


porphyrins, were detected in asphaltene fractions (Qian
et al., 2008b, 2010; McKenna et al., 2009). Vanadyl porphyrins
could be observed without asphaltene fractionation in samples
that contained significant amounts of vanadium (Hur et al.,
2010b). However, nickel porphyrins could be observed only
after the asphaltene fraction had been further separated by
thin-layer chromatography (Qian et al., 2010).

B. Combination With GCxGC


GCxGC is a technique in which two columns having different
polarities are connected in series for analysis. Compared to
conventional one-dimensional GC, in which either a polar or a
non-polar column must be selected, GCxGC is more efficient
at separating mixtures of compounds having polar and nonpolar functional groups. Therefore, GCxGC is a powerful tool
for the separation of complex mixtures (Hao et al., 2005;
Mondello et al., 2008). GCxGC MS can be a good complementary technique for FT-ICR MS because it can provide
quantitative information (Muller et al., 2012). Additionally,
GCxGC can provide information on non-polar compounds
that cannot be effectively measured by FT-ICR MS (Panda
et al., 2011; Cho et al., 2012a). Additionally, GCxGC can
provide information on non-polar compounds that may not be
effectively measured by FT-ICR MS (Panda et al., 2011; Cho
et al., 2012a).

VI. PEAK PICKING, MASS CALIBRATION, AND


CALCULATION OF ELEMENTAL FORMULAE
A. Algorithms for Peak Picking
Once the mass spectrum of a crude oil sample has been obtained,
interpretation begins with peak picking. Because of the wide
dynamic range of peaks present in the spectra of crude oils,
calculation of the proper noise level threshold and picking peaks
above the threshold is very important. This is because an
incorrectly calculated noise level threshold can cause valid
peaks to be lost or a significant amount of noise in the peak list.
Therefore, an algorithm employing automated peak picking
with a moving window of data points has been developed (Hur,
Oh, & Kim, 2009). With that algorithm, frequency domain mass
spectra are divided into many smaller segments based on a
predetermined number of data points. The noise level in each
segment is determined by a method originally used in the
THRASH algorithm (Horn, Zubarev, & McLafferty, 2000).
Using an automated algorithm having a moving window of data
points has provided quicker and more reliable peak-picking for
complex high-resolution data. In another approach, a combination of inverse Fourier transformation with a convolution
theorem was used to remove a rolling low-frequency baseline
and flatten it (Xian et al., 2010). This method is also effective for
automatic signal detection.

B. Equations and Procedures for Calibration


FIGURE 3. Comparison of the (a) total number of compounds and (b)
number of compounds in each chemical class identified in unfractionated oil
and combined SARA fractions. Reprinted (modified) with permission from
Cho et al. (2012c). Copyright (2012) American Chemical Society.

Mass Spectrometry Reviews DOI 10.1002/mas

Spectral calibration is another important step that affects the


accuracy of an analysis. As discussed in the previous section,
calibration of FT-ICR MS data is basically equivalent to
converting frequency domain spectra into m/z domain spectra.
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CHO ET AL.

Equations typically used for the conversion of frequency (f) to


m/z are given below (Ledford, Rempel, & Gross, 1984; Masselon et al., 2002; Zhang et al., 2005).
m a b
2
z
f f

m a b cI
2 2
z
f f
f

where I is the abundance of the m/z species and a, b, and c are


calibration factors.
The calibration factors can be determined by analyzing
standard samples with known masses. Calibration is generally
done using internal calibrants; typical calibration procedures are
as follows. Samples are analyzed with and without added
internal calibrants. Synthesized chemicals or commercial calibrant materials can be used as internal calibrants. The mixture of
crude oil and internal calibrants is first analyzed by highresolution mass spectrometry. The resulting spectra are processed, and the obtained peak lists are calibrated using the m/z
values of the internal calibrants. Elemental formulae are then
calculated from the calibrated peak list and are assigned based
on the m/z values within a 1 ppm error range. Typical conditions
used for petroleum data with these calculations for CcHhNnOoSs
are as follows: c unlimited, h unlimited, 0  n  5, 0  o  5,
0  s  4 (Kim, Rodgers, & Marshall, 2006). Among the
assigned elemental formulae, the most abundant classes (typically the homologous series of sulfur, hydrocarbon, or nitrogen
classes) are chosen, and theoretical mass values of the formulae
are calculated. The theoretical values are used to calibrate
spectra obtained without the added standards. After the spectra
are calibrated, elemental formulae are calculated from the
calibrated m/z numbers by the same method described above
and used for further interpretation.
In a typical procedure, the calibration factors are estimated
and applied over the entire mass range. Instead, Savory et al.
(2011) reported a walking calibration method in which a
spectrum is divided into segments and calibration factors are
determined and applied to each segment. By adapting the
walking calibration procedure, systematic errors with respect to
m/z were removed, and hence more accurate assignments with
reduced RMS error were achieved (Savory et al., 2011).

VII. GRAPHICAL METHODS FOR DATA


INTERPRETATION
The complexity of petroleum inevitably results in complex highresolution mass spectra. A high-resolution spectrum of crude oil
can routinely contain up to 30,000 peaks. If a crude oil sample is
analyzed using several different ionization sources, such as ()and ()-mode ESI and APPI, the number of peaks then gets
multiplied by the number of ionization sources used! In that
case, one may have to deal with over 100,000 peaks for a single
crude oil sample. Therefore, it is not surprising that development
of data interpretation methods has played a crucial role in the
study of crude oils by high-resolution MS.

A. Interpretation With Kendrick Mass Defect Analysis


Kendrick mass and van Krevelen analyses have been widely
used for data interpretation (Hsu, Qian, & Chen, 1992; Hughey

254

FIGURE 4. Kendrick mass defect versus nominal Kendrick mass for visual
interpretation. Note the visual vertical separation of compound classes (e.g.,
N vs. NO) and types (compounds with different number of rings plus double
bonds) based on mass defect and the simultaneous visual horizontal
distribution of number of CH2 groups for a given compound class and type.
Reprinted with permission from Hughey et al. (2001b). Copyright (2001)
American Chemical Society.

et al., 2001b; Kim, Kramer, & Hatcher, 2003). The Kendrick


mass is calculated by multiplying the observed m/z values by
14.00000/14.01565 (the monoisotopic mass of CH2) (Kendrick,
1963). The KMD is calculated by subtracting the Kendrick mass
from the nominal Kendrick mass. Therefore, in principle, the
digits after the decimal point for the Kendrick mass define the
KMD values; these do not change by adding or subtracting
(CH2)n from a given molecular formula. For example, if there is
a set of mass numbers differing by the mass of (CH2)n, their
Kendrick mass values will differ from each other only by whole
numbers; the fraction will remain the same, and hence their
KMD values will be the same. However, for mass numbers
differing by (2H)n and/or heteroatoms, their Kendrick mass
values will differ from each other by both whole numbers and
fractions. Therefore, they will have different KMD values. In
summary, each series of peaks differing only by (CH2)n but with
the same degree of unsaturation and heteroatom class will have
the same and their own unique KMD value. An example of
KMD plot is provided in Figure 4 (Hughey et al., 2001b).
Any neutral building blocks (e.g., COOH or H2) can be
used instead of CH2 to calculate KMD values. The tremendous
advantage of KMD analysis is that it is possible to group
calibrated m/z values according to their classes and/or degree of
unsaturation, even before their elemental compositions have
been calculated and assigned (Hughey et al., 2001b).
Kendrick mass defect (KMD) analysis has been extended to
higher-order mass defect analysis (Roach, Laskin, & Laskin,
2011). In this approach, peaks identified from spectra are
Mass Spectrometry Reviews DOI 10.1002/mas

METHODS FOR PETROLEOMICS

grouped by KMD values (e.g., by the CH2 series), and then the
groups are further sorted by the second KMD series (e.g., by the
H2 series). A group of peaks in different classes can be easily
identified by plotting the CH2-based KMD value as the abscissa
and the ratio of the CH2-based KMD and H2-based KMD of the
CH2-based KMD as the ordinate.

B. Application of van Krevelen Diagrams


The van Krevelen diagram was originally constructed for data
obtained by bulk elemental analysis (van Krevelen, 1950).
Kim, Kramer, and Hatcher (2003) applied it to elemental
compositions obtained by FT-ICR MS (Kim, Kramer, &
Hatcher, 2003). The concept was later expanded to threedimensional graphs (Wu, Rodgers, & Marshall, 2004). A van
Krevelen diagram is constructed from an elemental formula
by plotting the molar ratio of hydrogen-to-carbon (H/C ratio)
as the ordinate and the molar oxygen-to-carbon ratio (O/C
ratio) as the abscissa. In this way, each peak observed in a
crude oil spectrum is represented as a dot in the diagram.

&

Additionally, the relative abundance observed in a given


spectrum can be color-coded. Van Krevelen diagrams constructed from crude oil spectra are presented in Figure 5 (Bae
et al., 2010). These diagrams can be constructed for each
heteroatom class; they are particularly effective for displaying
and comparing classes having different numbers of heteroatoms. The N1 and N2 classes of compounds are compared in
the example shown in Figure 5.
Kendrick mass defect (KMD) plot is effective when
comparison of overall peak distribution is intended. Van
Krevelen diagram is effective when comparison of selected
peaks containing the same elements but different numbers (e.g.,
comparison of N1, N2, and N3 classes) is intended.

C. Double-Bond Equivalence Versus Carbon


Number Plot
The double-bond equivalents (DBEs) versus carbon number plot
is another widely used way of plotting crude oil spectra. DBEs
represent the number of double bonds and rings in a given

FIGURE 5. Van Krevelen diagram of the N1 and N2 class compounds detected in (a) a positive-mode ESI
spectrum of USSO, (b) a positive-mode ESI spectrum of the conventional oil, (c) a negative-mode ESI spectrum
of USSO, and (d) a negative-mode ESI spectrum of a conventional oil. (e) Suggested structures of N1 and N2 class
compounds are based on their DBE distributions. Reprinted with permission from Bae et al. (2010). Copyright
(2010) American Chemical Society.

Mass Spectrometry Reviews DOI 10.1002/mas

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CHO ET AL.

both synthetic and natural compounds (Hsu et al., 2011; Lobodin, Marshall, & Hsu, 2012). The compositional boundary of
hydrocarbon compounds in DBE versus carbon number plot is
shown in Figure 8. The compositional boundary is defined as the
absolute upper boundary of the DBE and is the carbon number
plus one. The boundary can be used as a way to assign elemental
formulae to a given mass. It has been reported that 10% of the
possible elemental formulae for masses below 1,000 Da can be
excluded by applying the concept of compositional boundary.

VIII. STATISTICAL INTERPRETATION OF CRUDE


OIL SPECTRA
A. Application of PCA, HCA, and Heat-Map Analysis

FIGURE 6. Plot of double bond equivalents versus carbon number for the
CnH2nzO2, CnH2nzO3, CnH2nzO4, and CnH2nzO5 species present within
the Athabasca oil sands sample. Where overlap occurs between species of
differing oxygen content, a particular DBE, and carbon number, the relative
intensities of the species have been summed; the values have also been
normalized. Reprinted with permission from Barrow et al. (2009). Copyright
(2009) American Chemical Society.

molecular formula and can be calculated by the following


equation for elemental formulae CcHhNnOoSs:
h n
DBE c  1
2 2

As for the van Krevelen diagram, each molecular formula


can be represented as a color-coded dot depending on its relative
abundance. An example of DBE versus carbon number plot is
shown in Figure 6 (Barrow et al., 2009). The DBE is useful for
compounds mainly composed of carbon and hydrogen and it
does not denote double bonds between other elements, such as
sulfur and oxygen (Kind & Fiehn, 2007).
Structural interpretation is also possible by use of the DBE
versus carbon number plot (Kim & Kim, 2010). The concept of
planar limits is a good example of structural interpretation.
Examples of planar limits are displayed in Figure 7. Planar
limits are defined as lines that connect maximum observed DBE
values with specific carbon numbers (Purcell et al., 2010; Cho,
Kim, & Kim, 2011). The slopes and intercepts of the planar
limits depend on the structural features of the observed peaks.
Let us assume that a given molecule is modified by the linear
and nonlinear addition of a series of saturated cyclic rings and
benzene rings. When the resulting formulae by addition are
plotted as a DBE versus carbon number plot, each series will
have its own specific slope value. The addition of saturated
cyclic rings results in a slope of 0.25, linear addition of benzene
ring, 0.75, and nonlinear addition of benzene rings, 1. Therefore,
planar limits can serve as a tool to predict the most condensed
molecular structure of a given mixture. The planar limits for
high-resolution spectra of fractionated SARA samples have
been studied. It was found that the planar limits obtained from
the spectra of the fractions matched well with the simulated
ones. Structures of molecules existing in the various fractions
were proposed based on a comparison between simulated results
and the observed values (Fig. 7).
Compositional boundary is another important concept that
has been deduced from the DBE versus carbon number plot for

256

One of the ultimate goals of petroleomics is to understand and


predict the chemical and/or physical behaviors of crude oils.
Therefore, it is important to identify the relationships between
high-resolution mass spectra and the chemical and/or physical
properties of crude oils. However, understanding these relationships cannot be accomplished by studying only a few crude oil
samples. Instead, many crude oil spectra must be analyzed and
interpreted. As stated in the previous section, high-resolution
MS analysis of a single crude oil sample can yield over 100,000
peaks. If more than ten samples of that complexity are analyzed,
one would have to assess millions of peaks. Therefore, extracting relational information between observed peaks and the
properties of crude oils poses a great analytical challenge.
Statistical analyses have been successfully used to better
understand large data sets, and hence one expects that statistical
analyses can play an important role in the study of petroleomic
data.
Principal component analysis (PCA) has also been used
earlier for the analysis of petroleum and related samples (Stout,
Uhler, & McCarthy, 2001; Eide et al., 2006; Malmquist
et al., 2007; Barrow et al., 2009; Tomasi & Christensen, 2009).
Hur et al. (2010a) developed a program specifically designed for
the statistical analysis of crude oil spectra and applied it to study
20 different samples. Figure 9 shows the results of PCA of these
samples. PCA successfully grouped the samples based on their
chemical compositions and enabled the display and identification of overall compositional differences between the samples.
Hierarchical analysis (HCA), another statistical method, was
also successfully used to group and compare the samples.
Subsequent heat-map analyses revealed differences among
grouped samples at the molecular level. Recently, the statistical
analysis has been applied to high-resolution FT-ICR MS data to
identify a source of environmental contamination caused by
heavy oil spill (Corilo et al., 2013).

B. Validation of a Fundamental Assumption of


Petroleomics by a Correlation Method
The validity of the assumption that the spectral findings are
related to crude oil properties has been tested statistically (Hur
et al., 2010b). The assumption is very important for petroleomics because if it is not valid, the practical usefulness of
petroleomics will be greatly limited. To test the assumption, the
correlational relationships between peaks identified by highresolution MS and the chemical/physical properties of crude oils
were investigated. Spearman rank correlation was used because

Mass Spectrometry Reviews DOI 10.1002/mas

METHODS FOR PETROLEOMICS

&

FIGURE 7. DBE versus carbon number plots generated from S1 class compounds observed in (a) saturates, (b)
aromatics, (c) resins, and (d) asphaltenes fractions. The slopes and y-intercepts of the lines and suggested
molecular structures of S1 class compounds found in each fraction are noted. Reprinted (modified) with permission
from Cho et al. (2011). Copyright (2011) American Chemical Society.

prior knowledge of a probability distribution is not required for


this correlation method. The correlational analysis was performed between spectral information and the sulfur contents of
crude oils, and the result was presented using a Circos diagram
(Fig. 10). The Circos diagram, originally developed for genomic
research, is a very effective tool for visualizing results from the
statistical analysis of crude oil spectra. In the diagram, the
outside shell designates heteroatom classes. The layer just inside
the class shell shows double-bond equivalences and carbon
number distribution for each class. The circle at the center shows
the distribution of the correlation coefficient (F). The lines in the
innermost circle are color-coded according to their F values.
Strong positive correlations are red and orange, weak or no
correlations are light green, and strong negative correlations are
green and blue.
Mass Spectrometry Reviews DOI 10.1002/mas

In the sulfur correlation diagram (Fig. 10a), sulfur-containing classes (e.g., S, S2, SO, and NS) are dominant and the color
of the lines located inside the correlation circle of the classes is
primarily either orange or red, indicating strong positive
correlations. One expects that compounds with sulfur atoms will
show a strong positive correlation with the sulfur content of the
samples, and that is exactly what is observed in the figure.
Additionally, nitrogen-containing compounds showed strong
positive correlations with the nitrogen content (Fig. 10b) and
oxygen-containing compounds with the total acid number
(TAN) of the crude oils. This result agrees well with the previous
report where good correlation between () ESI FT-ICR MS
data and the measured TAN has been shown (Qian et al., 2008a).
Therefore, this study clearly proves that correlational
relationships exist between mass spectrometric peaks and

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FIGURE 8. DBE versus carbon number plot for hydrocarbons, CcHh. The
blue line (DBE 0.9  C#) defines the upper compositional boundary for
fossil hydrocarbons. The green line (DBE C#) applies to all hydrocarbons
(including synthetic polyynes), and the red line (DBE C# 1) represents
the absolute upper limit for organic compounds that lack H and N atoms.
Reprinted with permission from Lobodin, Marshall, and Hsu (2012).
Copyright (2012) American Chemical Society.

FIGURE 10. Circos diagrams showing correlations between oil compounds


observed in () APPI FT-ICR mass spectra and bulk (a) sulfur and (b)
nitrogen content. Reprinted with permission from Hur et al. (2010b).
Copyright (2010) American Chemical Society.

properties of crude oils. This opens the door for chemicalcomponent-based prediction of the properties of crude oils.

IX. CONCLUSIONS AND FUTURE STUDIES

FIGURE 9. Score (a) and loading (b) plots are shown for PCA of 20 APPI
positive-mode spectra. Reprinted with permission from Hur et al. (2010a).
Copyright (2010) American Chemical Society.

258

The application of FT-ICR to the analysis of crude oils has


greatly improved the knowledge of these materials at the
molecular level. However, many issues still remain concerning
the analysis of these complex mixtures. Future research will
likely focus on (i) instrumental development to achieve higher
mass resolution, (ii) combining information provided from the
various ionization techniques, (iii) achieving more quantitative

Mass Spectrometry Reviews DOI 10.1002/mas

METHODS FOR PETROLEOMICS

information, and (iv) comparing and combining data obtained


with other techniques such as ion mobility mass spectrometry
(Fernandez-Lima et al., 2009; Ahmed et al., 2010, 2014).
Technological advances in FT-ICR MS instrumentation, ionization techniques, and data interpretation methods will be critical
for the advancement of petroleomics. For future progress, it is
very important to first fully understand the current state of the
various technologies. This review is intended to help researchers who have just entered the petroleomics research area.

ACKNOWLEDGMENTS
This work was supported by National Research Foundation of
Korea (NRF-2012R1A2A2A01044853) and: by the project
entitled Oil Spill Environmental Impact Assessment and
Environmental Restoration (PM57431) funded by the Ministry
of Oceans and Fisheries of Korea.

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