Friday, May 17, 2024



Structural Elucidation

Mass Spec Lab invites projects in MS structural elucidation of small molecules, polymers, biolipids, oligonucleotides, and oligosaccharides, benefiting from the combined structural characterization experience of our Mass Spec Lab experts.

Accurate mass spectrometry adds a layer of knowledge often needed to elucidate what exactly is contained within your unknown chromatographic peak.  Mass Spec Lab is an ideal partner for molecular structural elucidation using high resolution and high mass accuracy instrumentation. Our Ph.D. scientists have experience in small and large molecule applications and have a commitment and track record of solving difficult problems.  The value added by our years of practical experience in solving a range of structural elucidation problems cannot be underestimated.  

Small molecule structural elucidationis built on a foundation of high accuracy mass measurements which are acquired at Mass Spec Lab with a Waters G2-S quadrupole time of flight (QTof) mass spectrometer.  Accurate mass data allow elemental composition searching and isotopic pattern matching of molecular and fragment ion masses which can often lead to the identification of a specific elemental composition (e.g. experimental mass 122.0483 amu yields C6H6N2O with theoretical mass 122.0480 amu) consistent with the data.

Elemental composition is only the first step in structural elucidation, as one elemental composition represents a significant number of viable chemical structures. For example, 163 structures were identified in the ChemSpider database with chemical formula C6H6N2O.  Consequently, the next significant challenge is to trim the viable structure list and this requires covalent bond structure characterization.  At Mass Spec Lab, this is aided by MSE, an optimized MSMS acquisition mode that is unique to the G2-S QTof spectrometer.  MSE yields complete fragment ion information for every significant chromatographic peak in one analytical run.  

Experimental fragment ion data require expert interpretation.   For interpretation we utilize an extensive library of small molecule and fragment ion databases (e.g. NIST, ChemSpider, Metlin, mzCloud, Progenesis Meta Scope) and small molecule fragment analysis software, such as Mass Fragment (Waters), and Mass Frontier (Thermo).  Mass Frontier is an in silico-based, i.e. predictive, fragmentation elucidation software that generates structures of expected fragments from a given precursor ion. Mass Frontier draws on predictive algorithms as well as empirical fragmentation libraries based on published small molecule fragmentation mechanisms. These softwares predict fragment ions as well as their pathways of formation.(See our case study “Are Raw Material Contaminants Compromising Your Final Product“ for a demonstration of structural elucidation at the covalent bond level using Mass Frontier).

Mass Spec Lab brings together an impressive array of tools which are essential for success in structural elucidation.We not only have the instrumentation, personnel, and software needed for success, we also have the right philosophy.  We believe successful problem solving resides in customizing services to each client’s individual needs. We work with our clients to ferret out supplementary chemical data from other sources when necessary and integrate these data with MS data to solve the problem.

We can help you with difficult structural elucidation challenges. Request more information or call us at 949-872-2724.

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