The Key to Sound Organic Compound Analysis


The discovery and development of new drugs costs millions of dollars and can take many years to reach the commercial market. With complex and continuously more potent drugs, the role of analytics is critical to determine the health of the molecule under development, the number of impurities, as well as its efficacy and safety to not only meet cGMP guidelines but also to receive FDA approval.

During the early stages of discovery involving identification, selection and optimization of drug candidates, the application of liquid chromatography coupled with mass spectrometry (LC/MS) assays is one of the most powerful analytical tools for organic compound analysis and have become extremely useful in accelerating the transition from discovery to pre-clinical stages of chemistry development. Since it helps to identify impurities and other problems in the chemistry from the earliest stages, this analytical technique, in conjunction with proper in vitro and in vivo studies, can significantly shorten timelines and reduce costs. This article provides an overview of LC/MS.

What is LC/MS?

Liquid chromatography/mass spectrometry (LC/MS) is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry. The integration of these two techniques are popular in chemical analysis because the individual capabilities of each are enhanced by the other.

While liquid chromatography separates mixtures with multiple components, mass spectrometry provides structural identity of the individual components, including biochemical organic and inorganic compounds, with high molecular specificity and detection. An LC/MS system contains an interface that efficiently transfers separated components from the LC column into the MS ion source.

In API manufacturing, the LC/MS methodology is used to accomplish the following:

  • Reaction process monitoring by mass changes and changes in isotopic concentration.
  • Trace impurity determination by MS (side-reactions).
  • Polymer modification for use in pre-clinical studies.
  • Identification and characterization of impurities.
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LC/MS versus HPLC

While here are PCI Synthesis, the preferred analytical method is LC/MS, the alternative is high performance liquid chromatography (HPLC), a form of column chromatography that pumps a sample mixture or analyte in a solvent at high pressure through a column.

We believe that the key advantages of using LC/MS methods over HPLC methods include:

Selectivity. With LC/MS co-eluting peaks can be isolated by mass selectivity and are not constrained by chromatographic resolution.

Peak assignment. A chemical fingerprint for the compound of interest is generated, ensuring correct peak assignment in the presence of complex matrices.

Molecular weight information. LC.MS methods can ensure confirmation and identification of known and unknown compounds.

Structural information. Controlled fragmentation enables structural elucidation.

Rapid method development. Provides easy identification of eluted analytes without retention time validation.

Sample matrix adaptability. Decreases sample preparation time.

Quantitative and qualitative data  Both types of data can be obtained easily with limited instrument optimization.

Here’s how we do it

At PCI Synthesis we use an Agilent 6230 Q-TOF LC/MS system to have full-spectrum, high-resolution, accurate-mass data for screening, profiling and identifying anything from small molecules to large biologic compounds. This system enables us to perform mass analysis of compounds and is designed to work in conjunction with HPLC-UV to determine the purity and the subsequent molecular weight of each fraction including relative isotopic abundance. The Agilent LC/MS system is flexible enough to handle most common methods of mass spectrometry, including:

  • Various ionization sources such as Agilent DualJet ESI (hard) or Chemical ionization (soft).
  • The ability to detect in both positive and negative ion mode with fast polarity switching.
  • The ability to measure molecular weights ranging from 120Da to 22,000Da.

At PCI Synthesis we are constantly exploring to ensure we are providing the most innovative analytical methods. We have found that Liquid Chromatography combined with mass spectrometry has proven to be a highly effective technique for analyzing compounds.