Identification of "known unknowns" utilizing accurate mass data and ChemSpider.

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Note: The final approved version of this paper can be found at www.springerlink.com,
http://dx.doi.org/10.1007/s13361-011-0265-y. This is a prepress version of the article.
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Identification of “Known Unknowns” Utilizing Accurate Mass Data and ChemSpider

James L. Little,1 Antony J. Williams,2 Alexey Pshenichnov,2 Valery Tkachenko2
1Eastman Chemical Company, Kingsport, TN 37662, USA
2ChemSpider, Royal Society of Chemistry, Cambridge, UK

Correspondence to: J. L. Little; e-mail: jameslittle@eastman.com, Antony J. Williams; e-mail:
williamsa@rsc.org

Abstract
In many cases, an unknown to an investigator is actually known in the chemical literature,
a reference database, or an internet resource. We refer to these types of compounds as
“known unknowns.” ChemSpider is a very valuable internet database of known
compounds useful in the identification of these types of compounds in commercial,
environmental, forensic, and natural product samples. The database contains over 26
million entries from hundreds of data sources and is provided as a free resource to the
community. Accurate mass mass spectrometry data is used to query the database by
either elemental composition or a monoisotopic mass. Searching by elemental
composition is the preferred approach. However, it is often difficult to determine a
unique elemental composition for compounds with molecular weights greater than 600
Da. In these cases, searching by the monoisotopic mass is advantageous. In either case,
the search results are refined by sorting the number of references associated with each
compound in descending order. This raises the most useful candidates to the top of the
list for further evaluation. These approaches were shown to be successful in identifying
“known unknowns” noted in our laboratory and for compounds of interest to others.



e have previously demonstrated [1]
that searching the Chemical
Abstracts Service (CAS) Registry
employing accurate mass mass spectrometry
data is a very useful approach for the
identification of “known unknowns.” We define
a “known unknown” as a compound which is
unknown to the investigator but is known in the
chemical literature, a reference database, or an
internet resource.

There is a particular need for additional
approaches for the identification of “known
unknowns” found in liquid
chromatography/mass spectrometry (LC/MS)
analyses because the availability of computer
searchable collision-induced dissociation (CID)
mass spectral databases is limited for LC/MS [1]
as compared to that of electron ionization (EI)
mass spectral databases. We have found that
searching “spectraless” databases such as the
W

2

CAS Registry [1] by elemental compositions or
molecular weights then sorting the hit list in
descending order by the number of associated
references to be very effective in the
identification of “known unknowns.” The most
likely candidates are normally brought to the
top of the list where they can be further
scrutinized by employing additional data.

ChemSpider is another very large “spectraless”
database that can be searched by elemental
composition, molecular weight, or
monoisotopic mass and it is provided as a free
resource to the community. ChemSpider
contains >26 million entries as compared to the
CAS Registry that contains >62 million
substances. In our current work, the
ChemSpider interface was modified [2] such
that the initial search results can be sorted by
the number of references associated with an
entry. The approach was then evaluated with a
wide variety of compounds and compared to
previous results obtained with the CAS Registry
[1].

Experimental

ChemSpider Software Modifications

Several changes were made in the ChemSpider
software interface to facilitate our studies [2].
The most important change was the ability to
sort the initial search results in descending
order by the number of data sources or
associated references. The references in
ChemSpider originate from the SureChem
patent database (>20 million), PubMed (>20
million articles), and the content of the Royal
Society of Chemistry publishing database. In
our work, sorting the “# of References” column
was found to be the most useful. Many screen
displays of the software annotated with
examples from our laboratory are shown in the
Electronic Supplementary Material.

Two other changes allowed more convenient
data entry for searching by the user. The first
change was the ability for the user to enter the
m/z value directly for a charged species and
then select the type of ionic species from a pull-
down (drop-down) menu. Examples of typical
types of ionic species in the menu include [M +
Na]+, [M + NH4]+, [M - H]-, etc. The m/z value
entered is then automatically adjusted by the
program before searching the monoisotopic
mass of the neutral species as it would appear
in the ChemSpider database.

The second change was the ability for the
entered m/z value of the charged species to be
corrected for the mass of an electron. Some
manufacturers’ data systems do not properly
calculate the m/z values of ions for the mass of
an electron [3, 4]. The errors normally cancel
within the manufacturers’ elemental
composition programs because the reference
calibration tables are also not corrected.
However, all data exported into other
applications for further data processing should
be corrected.

Acquisition of Accurate Mass Data

The experimental detail including calibrations,
typical chromatographic separations, and
sample preparations were previously described
in detail [1]. Briefly, the accurate mass
electrospray LC/MS/UV-Vis (ultraviolet-visible)
data were obtained on a LCT time-of-flight mass
spectrometer (Waters Corporation, Milford,
MA) equipped with a LockSpray secondary ESI
probe. An 1100 Series liquid chromatograph
with autosampler, degasser, and UV-Vis diode
array spectrophotometer (Agilent Technologies,
Santa Clara, CA) was employed for the
separations in the reversed phase mode. The
UV-Vis spectral data is very useful in locating
particular classes of compounds (UV absorbers,
dyes, etc.) and in confirming the identity of
compounds by comparison to reference spectra
from standards, literature references, or even
internet sources.

Elemental compositions were generated from
monoisotopic masses utilizing the Waters
Elemental Composition Program within

3

MassLynx V4.1 software which included i-FIT
software for numerically ranking the observed
isotopic pattern to the theoretical ones. Our
LCT accurate mass measurements typically
yielded a standard deviation of 5 ppm. Thus,
windows of +/-18 ppm (slightly greater than 3
standard deviations) were employed in
examples from our laboratory to insure
inclusions of all reasonable candidates for
determining elemental compositions or for
searching ChemSpider by monoisotopic masses.
In literature studies, windows of approximately
+/-5 ppm were employed because many
currently available accurate mass time-of-flight
instruments yield standard deviations
approaching 1 ppm for mass measurements.

Results and Discussion

Descriptions of Two Approaches

The ability to search by either elemental
composition or monoisotopic mass is very
valuable for the identification of “known
unknowns” using accurate mass mass
spectrometry data. In the work described
within this article, the ChemSpider user
interface was modified to permit the sorting of
either the elemental composition or
monoisotopic mass search results by the
number of associated references. The results,
sorted in descending order, normally bring the
most useful entries to the top of the list. These
candidate structures are then scrutinized [1] by
other available data such as in-source CID
spectra, UV-Vis spectra, GC/MS data, number of
exchangeable protons, NMR data, etc. to
ultimately obtain the identification of the
compound of interest. For critical
identifications, a standard of the material is
normally obtained and its LC retention time,
UV-Vis spectrum, and in-source CID spectra are
compared to those of the unknown.

A very similar approach [1] was demonstrated
to be very useful utilizing the CAS Registry of
>62 million substances, a fee-based service,
which is searched by either STN Express or the
web-based version of SciFinder. The CAS
Registry can only be searched by elemental
composition, molecular weight, or nominal
molecular weight, but not monoisotopic mass.
The ability to search by the monoisotopic mass
is much more useful because the standard
deviation for its determination is much lower
than that for the molecular weight. In addition,
the monoisotopic mass is calculated by all
manufacturers’ data systems whereas the
molecular weight must be manually calculated
by the user.

One significant advantage of searching the CAS
Registry versus the ChemSpider database is the
ability of the former to search its > 34 million
document records associated with an elemental
composition by key words [1]. Only very
minimal sample history is required to quickly
obtain useful candidates for tentative
identifications by this approach. This capability
can be especially useful in identifying more
obscure “known unknowns” with fewer
associated references. This capability is not
currently available with ChemSpider.

Evaluation of the Two Approaches with
Literature Examples

A group of 90 compounds was assembled from
literature sources [5-8], internet sites, and
American Society of Mass Spectrometry
Conference presentations to evaluate the two
approaches in ChemSpider. The results are
summarized in Tables 1 and 2. Searching the
ChemSpider database by elemental
compositions then sorting in descending order
by the number of overall references yielded
more target compounds highly ranked as
compared to the same approach using
monoisotopic masses. This is to be expected
because the number of overall candidates was
less when searching by elemental composition
(mean = 513, median = 310) compared to
monoisotopic mass (mean = 800, median =
740). However, the overall number with
rankings less than or equal to 5 was acceptable
in both cases. Thus, searching by elemental

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composition is the preferred approach, but
searching by a monoisotopic mass is also a
reasonable approach when a unique elemental
composition cannot be readily determined.

Table 1. Searching ChemSpider by elemental composition then sorting by number of associated
references.

Class of Compounds
Number
Compounds
in Class
Position of Compound Sorted in Descending
Order by Number of References
#1 #2 #3 #4 #5 >#5
Drugs 45 43 1 1
Pesticides 8 7 1
Toxins 2 2
Polymer antioxidants 15 15
Polymer UV Stabilizers 10 8 1 1
Polymer Clarifying agent (Irgaclear DM) 1 1(14)
Polyurethane additives 4 2 1 1
Natural products 3 2 1
Herbicide (clofibric acid) 1 1
Artificial sweetener (Sucralose) 1 1
Total Compounds ChemSpider 90 81 4 3 1 1
Total Compounds CAS Registry [1] 90 84 4 1 1

Table 2. Searching ChemSpider by monoisotopic mass with +/- 5 ppm window.

Class of Compounds
Number
Compounds
in Class
Position of Compound Sorted in Descending
Order by Number of References
#1 #2 #3 #4 #5 >#5
Drugs 45 43 1 1
Pesticides 8 7 1
Toxins 2 2
Polymer antioxidants 15 13 1 1
Polymer UV Stabilizers 10 6 1 1 1 1(8)
Polymer Clarifying agent (Irgaclear DM) 1 1
Polyurethane additives 4 2 1 1
Natural products 3 2 1
Herbicide (clofibric acid) 1 1
Artificial sweetener (Sucralose) 1 1
Total Compounds ChemSpider 90 77 4 4 2 3

The same 90 compounds were previously
evaluated with the CAS Registry searching by
elemental compositions [1] using the web-
based version of SciFinder. Similar results (see
bottom of Table 1) were obtained using either
ChemSpider or the CAS registry as databases for
these limited number of test compounds. The
CAS Registry currently cannot be searched by
monoisotopic mass [1], therefore, no direct
comparison can be made in Table 2 for the
results obtained with ChemSpider.

5

Example from Our Laboratory for UV Stabilizer
Identification in a Commercial Polymer
An unknown additive, noted in a commercial
polymer sample, was characterized by accurate
mass LC/MS. The accurate mass data was used
in conjunction with isotopic abundance
information to obtain an elemental composition
of C22H29N3O. ChemSpider was searched by the
elemental composition and 1135 hits were
found which were sorted in descending order
by the number of overall associated references.
The top candidate was Tinuvin 328. The
proposed structure was consistent with the
accurate mass in-source CID spectrum (Scheme
1) which showed two very significant losses of
C5H10 from the protonated molecule, [M + H]+,
and the presence of a C5H11+ ion at a m/z value
of 71.085.



Scheme 1. In-source CID fragmentation for Tinuvin 328

The confidence afforded by the initial data
allowed the identity to be reported to the
customer. At a later date, the identification of
the additive was confirmed by comparison of its
LC retention time, UV-Vis spectrum, and in-
source CID mass spectra to those of a
purchased reference sample.

ChemSpider was also searched for protonated
molecules with m/z 352.239 using a m/z
window of +/-18 ppm. There were 1459 hits
and Tinuvin 328 was still the top candidate. The
mass precision of our older instrumentation is
relatively large, but newer time-of-flight
instrumentation afford much better mass
precision, which would return a smaller number
of candidates from the search. Screen displays
from the ChemSpider interface for the
identification of Tinuvin 328 by both
approaches are shown in the Electronic
Supplementary Material.

Advantage of Searching Higher MW Compounds
by Monoisotopic Mass Data

It is often difficult to determine a unique
elemental composition for “known unknowns”
with molecular weights greater than 600 Da [9,
10]. Either there are two or more possible
elemental compositions for the unknown or
one is inadvertently excluded if the somewhat
subjective user settings are set too narrow for
elements present, range of elements, double
bond equivalents, etc. In theory, the number of
elemental compositions increases dramatically
as the molecular weight increases. However, in
practice, the number of elemental compositions
at molecular weights greater than 600 Da
decreases dramatically in both ChemSpider (see
Figure 1) and CAS Registry databases [1].

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Figure 1. Number of ChemSpider entries versus molecular weight ranges

Therefore, it is much more reasonable to search
for “known unknowns” in these databases using
monoisotopic mass instead of struggling to
determine a unique elemental composition for
searching. The rankings noted by number of
references for several higher molecular weight
compounds noted in the literature [9,10] are
compared to elemental composition searches
versus monoisotopic mass searches in Table 3.
There is essentially no significant penalty noted
for searching by monoisotopic mass instead of
elemental composition for this limited number
of examples. Of course, ex post facto, it is still
extremely important to compare the isotopic
abundances of the candidate structures from
ChemSpider to those of the unknown. The
ability to calculate, rank, and compare
theoretical isotopic abundances for elemental
compositions to those of observed ones is
normally a standard option in most mass
spectrometry manufacturers’ software. The
CAS and ChemSpider identification numbers for
compounds in Table 3 are included in the
Electronic Supplementary Material.


0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
7,000,000
8,000,000
No
. o
f C
om
po
un
ds
Molecular Weight Ranges

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Table 3: Comparison of Results Searching Compounds MW>600 Da by Elemental Composition and
Monoisotopic Mass
Compound Elemental Composition
Monoisotopic
Mass
Rank
Elemental
Composition
Rank Monoisotopic
Mass using +/-5 ppm
window
Moxidectin C37H53NO8 639.3771 1 of 5 1 of 39
Erythromycin C37H67NO13 733.4612 1 of 42 1 of 53
Digoxin C41H64O14 780.4296 1 of 47 1 of 65
Rifampicin C43H58N4O12 822.4051 1 of 29 1 of 96
Rapamycin C51H79NO13 913.5551 1 of 43 1 of 51
Amphotericin B C47H73NO17 923.4878 1 of 33 1 of 42
Gramicidin S C60H92N12O10 1140.7059 1 of 5 1 of 13
Cereulide C57H96N6O18 1152.6781 1 of 3 2 of 8
Cyclosporin A C62H111N11O12 1201.8414 1 of 36 1 of 38
Vancomycin C66H75Cl2N9O24 1447.4302 1 of 24 1 of 26
Perfluorotriazine C30H18N3O6P3F48 1520.9642 1 of 1 1 of 1
Thiostrepton C72H85N19O18S5 1663.4924 1 of 5 1 of 5

Example from Our Laboratory for the
Identification of a Higher Molecular Weight
Antioxidant in a Commercial Polymer
An unknown additive, noted in a commercial
polymer sample, was characterized by accurate
mass LC/MS. The ammonium adduct, [M +
NH4]+, of the component was observed at a m/z
value of 801.558. The observed ion was
confirmed to be an ammonium adduct because
at higher in-source CID energies the ammonium
adduct intensity was reduced and the intensity
of the sodium adduct was noted to increase.
This increase in absolute intensity of the sodium
adduct and corresponding decrease in that of
the ammonium adduct is routinely noted in our
laboratory for in-source CID [1] and a typical
example is shown in the Electronic
Supplementary Material.

ChemSpider was searched by the monoisotopic
mass for the ammonium adduct with a mass
window of 18 ppm (see Electronic
Supplementary Material) and 23 candidates
were obtained. The top candidate was
Goodrite 3114. Only two of the 23 candidates
had isotopic abundances consistent with that of
the unknown. Of these two, only the in-source
CID mass spectrum (Scheme 2) of Goodrite
3114 was consistent with that for the unknown.

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Scheme 2. In-source CID fragmentation for Goodrite 3114

At a later date, the LC retention time, UV-Vis
spectrum, and in-source CID mass spectra of a
commercial sample were shown to be identical
to those of the unknown.

Future Enhancements to Improve Productivity

ChemSpider currently supports a web
application program interface (API) via web
services
(http://www.chemspider.com/MassSpecAPI.as
mx) for batch queries by external vendors’
programs. Several companies, including Bruker
Daltonics, Thermo Scientific, Waters, and
Agilent Technologies, integrate their data
processing programs with ChemSpider. Users
who integrate using the web services, including
these vendors, use a token supplied by
ChemSpider to authenticate their identity to the
web service. Currently there are no similar
capabilities for such queries of the CAS Registry
using either SciFinder or STN Express.

Some changes in both the current API and the
vendors’ programs would be required to utilize
associated references and comparison of
isotopic abundances to facilitate increases in
data processing speeds. When searching by
monoisotopic mass, the isotopic abundances of
the candidates should then be calculated in the
vendor’s data system and compared to the
observed isotopic abundance of the unknown
and sorted in descending order by either the
number of references or the fit of the isotopic
abundances to those of the unknown. This
would be particularly useful for “known
unknowns” with molecular weights greater than
600 Da, but would be also beneficial for lower
molecular weight compounds. Alternatively,
the ChemSpider software could be enhanced to
perform the calculations of the isotopic
abundances of the candidates for comparison
to the unknowns.

Even with the above changes, excessive time
would still be needed to manually compare the
observed CID spectrum of an unknown to

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fragments expected by the user from the
candidates’ structures. If in silico CID spectra,
i.e. theoretical fragmentation with predicted
abundances, could be calculated [11,12] and
ranked for the candidate structures from either
ChemSpider or SciFinder SDF (Structure Data
Format) files [13], further data processing
speeds would be realized. The results of the
numeric structure ranking, isotopic abundance,
and number of references could then be more
quickly examined by the user to yield tentative
identifications.

Both ChemSpider and the web-based SciFinder
are able to export structures for the candidate
compounds in SDF. The web-based version
SciFinder permits the export of up to 500
structures in an SDF file. There is no limit to the
number of structures that can be exported in
the ChemSpider API and a limit of 10,000 in the
web interface.

Charged Species in ChemSpider

More development work needs to be
performed to facilitate the searching of charged
species by either elemental composition or
monoisotopic mass. Sodium benzoate
illustrates the current state of affairs for organic
anions. Its elemental composition and
monoisotopic mass are listed in ChemSpider as
C7H5NaO2 and 144.018724, respectively. It
would be more useful to parse the elemental
composition as C7H6O2.Na (neutral benzoic acid
to left of period, associated cation to the right)
then list the elemental composition and
monoisotopic mass for searching as C7H6O2 and
122.037, respectively. This is the format
employed in the CAS Registry [1]. In reverse
phase chromatography electrospray mass
spectrometry, the organic anions elute as their
free acid form and are normally detected as [M
- H]- ions in the negative ion mode. Thus, their
identity is independent of their associated
cation.

A simple example of an organic cation is N,N,N-
trimethyl-N-benzylammonium acetate whose
elemental composition and monoisotopic mass
are listed as C12H19NO2 and 209.1216,
respectively, in ChemSpider. It would be more
beneficial to parse this type of organic cation as
C10H16N.C2H3O2 then list the elemental
composition and monoisotopic mass for
searching, respectively, as C10H16N and
150.1277.

Amphoteric (inner salt, zwitterionic) species are
listed in the database with no modifications.
For example, (CH3)3N+CH2CO2-, trimethylglycine,
is listed as C5H11NO2 with monoisotopic mass of
117.079. This type of compound would yield [M
+ H]+ and [M + acetate]- ions, respectively, in
positive and negative ion electrospray analyses
using acetate in the LC eluent. Thus the
elemental composition for the species would
need to be corrected before searching.

Conclusions

Modifications in the ChemSpider interface to
sort elemental composition and monoisotopic
mass search results by the number of
associated references in descending order
offered significantly improved capabilities for
the identification of “known unknowns” using
accurate mass mass spectrometry data. Other
changes were made to allow easier input of
data by users to specify the type of ion adduct
and to correct the monoisotopic mass for the
mass of an electron. Further enhancements are
still needed to improve the overall productivity
of the process and to enable the searching of
charged species.

The elemental composition search is the
preferred one in the lower molecular weight
range (200-600 Da), but even the monoisotopic
mass search with reasonable error windows is
viable in this range. Monoisotopic mass
searching for compounds with a molecular
weight >600 Da is preferred when it is difficult
to determine a unique elemental composition.
The resulting candidates from the monoisotopic
mass search are then ranked by comparing their
calculated isotopic abundances by the

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manufacturers’ isotope abundance programs to
that of the unknown.

The ability to search monoisotopic mass in
ChemSpider is an important function which is
absent in search engines for the CAS Registry.
However, CAS Registry searches can be further
refined by key words which can be particularly
useful for more obscure “known unknowns”
with few associated references. This option is
not currently available in ChemSpider. The
ability to search by both databases is very
desirable depending on the problem at hand
when costs are not a limitation. ChemSpider is
provided at no cost to the community, but
there is a fee associated with the utilization of
the CAS Registry.

In all cases, other data such as sample history,
UV-Vis data, types of ions observed,
exchangeable protons, CID spectra, etc. are
needed to scrutinize the candidate structures
from the elemental composition and
monoisotopic mass search results. For ultimate
confirmation of structure, analysis of a standard
material under identical conditions is always
desirable.

Acknowledgements
The authors gratefully recognize Curt Cleven
from Eastman Chemical Company, Mike Scott
from Agilent Technologies, Inc., and Jim
Lekander from Waters Corporation for their
help and advice. We also thank Bill Tindall and
Kent Morrill (retirees from Eastman Chemical
Company) for their initial work on “spectraless”
databases created from the TSCA (Toxic
Substances Control Act) and the Eastman
Corporate Plant Material databases.

References
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Identification of “known unknowns” utilizing
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Pshenichnov, A: Accurate mass measurements:
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ChemSpider. Proceedings of the ASMS, Denver,
CO, 2010.
3. Mamer, O. A.; Lesimple, A.: Common
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molecular weights. J.Am.Soc.Mass Spectrom.
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electron mass in the calculations of exact mass
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with UHR-TOF. Bruker Application Note # ET-23
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Electronic Supplementary Material for
DOI: 10.1007/s13361-011-0265-y
¾Identification of “Known Unknowns” Utilizing Accurate Mass Data and ChemSpider
¾Journal of the American Society for Mass Spectrometry, online version
¾James L. Little,a Antony J. Williams,b Alexey Pshenichnov,b Valery Tkachenkob
aEastman Chemical Company, Kingsport Tennessee, USA
bChemSpider, Royal Society of Chemistry, Cambridge, UK
¾Correspondence to jameslittle@eastman.com or williamsa@rsc.org
1

Initial Window Selected at www.chemspider.com on Internet
Either Select “More Searches”
or Select “Advanced Search”
2

Second Window Selected in ChemSpider Interface on Internet
Select “Advanced”
3

UV Stabilizer Example: Three Steps for Searching by Elemental Composition
1) Select “Search by Properties”
2) Enter elemental composition
3) Select “Search”
4