Special Issues-04-01-2007

The 30-year history of advances in gas chromatography–mass spectrometry technology continues today. Recent improvements in hardware, electronics, and data analysis software have resulted in new levels of productivity and sensitivity that have broadened the potential applications for this laboratory mainstay.

Mass spectrometers are effective for identifying and quantifying unknown molecules, such as disease-related proteins and small molecules in pharmaceutical research and medical diagnosis. In addition, mass spectrometry (MS) can be particularly powerful when analyzing molecules with complex structures, such as posttranslationally modified proteins. Among various MS approaches, high-resolution multistep tandem MS (MS-MS) is an emerging methodology for accurate identification of complex molecules. In this article, we describe a new approach for mass analysis with enhanced quantitative capability combined with high-resolution multistep MS-MS, where the dynamic range of quantitation covers four orders of magnitude.

The ability to perform accurate mass measurements in mass spectrometry (MS) for elemental composition determination (ECD, also known as formula identification) provides a powerful tool for assisting in the identification of unknown compounds. Recent advances in data processing methods have demonstrated the ability to obtain mass accuracy in the 5–10 ppm range on routine single- and tandem-quadrupole systems (1,2), sufficient to assist in the formula identification. However, even on more expensive high-resolution systems such as quadrupole time-of-flight (qTOF) or Fourier transform (FT)–MS instruments that are capable of routinely measuring mass accuracy in the 1–3 ppm range, the formula identification is not unique, particularly for higher molecular weight compounds. By calibrating instruments to obtain high spectral accuracy as well as mass accuracy, the ability to unambiguously identify the formula is improved substantially, particularly on low-resolution systems.

It makes intuitive sense - the higher the sensitivity of an inductively coupled plasma–mass spectrometry (ICP-MS) system, the lower the detection limit. But there are many factors that affect the detection limit for a given isotope in a given sample. These factors include sensitivity, background noise, and interferences.

Gas chromatography–mass spectrometry (GC–MS) and liquid chromatography (LC)–MS are widespread successful approaches, based on single-quadrupole MS, for the routine detection, identification, and quantitation of compounds. There has, however, been increasing interest in the use of tandem MS in more challenging, complex matrices such as those commonly found in food, environmental, and biological analyses. The combination of GC with tandem-quadrupole MS (MS-MS) is discussed, where the inherent increase in selectivity and sensitivity of the approach has enabled rapid, confident compound detection and quantitation for such demanding applications.

A common endpoint for a biomarker discovery experiment is a list of putative marker proteins. The next step is then to perform targeted quantitative measurements of these proteins in an expanded patient population to assess their validity as markers. Analytical accuracy and precision are required for unambiguous quantitative analysis of targeted proteins from very complex mixtures. Wide dynamic range and high sensitivity are critical for detecting low-abundance proteins. Such an assay also is appropriate for "targeted discovery" experiments, where the goal is to quantitate a large number (up to hundreds) of known proteins in a complex sample.