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Performing compositional analysis without fragmentation spectra: the spectral quality provided by the apex-Qeis essential for absolute molecular formula generation with isotopic analysis of organic molecules.

The ability of mass spectrometry to determine molecular composition is widely applicable to various disciplines including pharmaceutical discovery, metabolomics, petroleum analysis, geochemistry and environmental chemistry, among others.

Performing compositional analysis without fragmentation spectra is advantageous when measuring complex mixtures and is intrinsically faster, allowing higher throughput in many cases.

To facilitate molecular formula analysis, Bruker Daltonics has developed the generate molecular formula (GMF) tool within its DataAnalysis software package. When used with high performance mass spectrometers like the Bruker Daltonics apex-Qe high field Fourier transform mass spectrometer (FTMS) series, additional information fortifies the mass measurement to provide an extremely confident determination of the elemental makeup of a given peak. The GMF tool is based on robust statistical models using the masses, intensities, and spacing of each isotope in the measured distribution to determine the correct elemental formula for completely unknown organic molecules. This approach is valid for much higher molecular weight species where by "mass alone" there would be far too many candidate formulas.

The apex-Qe FTMS mass spectrometer is ideally suited for this type of molecular composition analysis because of its exact mass accuracy, precision and resolving power.

Methods and Results

To demonstrate the effectiveness of composition analysis using the GMF analysis tool, two sets of small molecule data were acquired using the apex-Qe. The first set of samples consisted of molecules under 600 Daltons, lincomycin hydrochloride, haloperidol and reserpine. The second set of samples were higher molecular weight molecules consisting of the macrolide roxithromycin and ionophore valinomycin. In both cases, external calibrations were applied to cover the mass range of 175 to 1700 Da. For each compound, GMF returned the proper elemental composition as the top choice.

Small Molecules

Our testing showed that in each case the GMF tool reported the correct elemental composition for the peak of interest without user intervention after a processing time of 1 to 4 seconds, depending on the number of potential candidates generated. Both the inherent mass accuracy and mass precision of the apexQe were shown to be integral to the simplification of small molecule analysis workflows, especially in cases like these where the expected compositions extend beyond CHON. With the accurate relative intensity information provided, the experiment was able to benefit fully from the ability of GMF to compare the measured isotopic intensity profile with that of each proposed formula.

Larger Organic Molecules

Several classes of organic molecules, such as macrolide antiobiotics, are found at a m/z larger than the compounds previously described and require that elemental analysis be carried out up to ~1500 m/z. To demonstrate the usefulness of the apex-Qe for these molecules, we analyzed two well known antiobiotics, roxirthromycin and valinomycin, on a 12-tesla ultra-high resolution apex-Qe. A comparison of the measured roxirthromycin spectra with the theoretical indicated the ability of the 12-tesla apex-Qe to provide robust isotopic profiles for larger ions, with GMF correctly indicating the empirical formula and showing that the molecule is not sodiated. GMF processing of the valinomycin spectrum indicated that the correct molecular formula was chosen and that the GMF tool correctly determined that the molecule at m/z 1133 was sodiated.


These data all illustrate the powerful combination of the intelligent generate molecular formula tool and the apex-Qe FTMS. The spectral quality provided by the apex-Qe is essential for absolute molecular formula generation with isotopic analysis of organic molecules. Additionally, utilizing the higher field advantage of the 12- or 15-tesla apex-Qe easily extends this advantage to the challenging analysis of larger organic molecules, formerly unreachable using conventional methodologies and platforms.


* Compositional analysis without fragmentation spectra allows higher throughput

* GMF analysis tool provides elemental makeup of a given peak

* apex-QE FTMS is suited for molecular composition analysis

* GMF tool is effective for both small and larger organic molecules


For additional information on the technologies discussed in this article, see Laboratory Equipment magazine online at or the following Web site:


Dr. Michael Easterling may be contacted at or by phone at 978-663-3660, ext. 1488.

Michael Easterling, Ph.D., FTMS Applications Manager
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Title Annotation:Separations/Spectroscopy
Author:Easterling, Michael
Publication:Laboratory Equipment
Date:Sep 1, 2006
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