Quantitative protein measurements by mass spectrometry have gained wide acceptance in research settings. However, clinical uptake of mass spectrometric protein assays has not followed suit. In part, this is due to the long-standing acceptance by regulatory agencies of immunological assays such as ELISA assays. In most cases, ELISAs provide highly accurate, sensitive, relatively inexpensive, and simple assays for many analytes. The barrier to acceptance of mass spectrometry in these situations will remain high. However, mass spectrometry provides solutions to certain protein measurements that are difficult, if not impossible, to accomplish by immunological methods. Cases where mass spectrometry can provide solutions to difficult assay development include distinguishing between very closely related protein species and monitoring biological and analytical variability due to sample handling and very high multiplexing capacity. This paper will highlight several examples where mass spectrometry has made certain protein measurements possible where immunological techniques have had a great difficulty. 1. Introduction Quantitative mass spectrometry of proteins has evolved dramatically over the last decade. Early methods involved labeling proteins with reagents enriched in stable isotopes in order to introduce mass tags into proteins of interest for relative quantification of proteins [1, 2]. These reagents have been refined over the years and have found widespread use in the form of the ITRAQ reagent [3]. Metabolic labeling of proteins with stable isotope-enriched amino acids has also been used as a technique for the relative quantification of proteins in cell culture systems [4]. Additionally, “label-free” methods have been developed for relative quantification of proteins in complex mixtures [5, 6]. As mentioned, these methods were developed for relative quantification of proteins, that is, comparing two or more samples and determining whether levels of proteins increased or decreased in response to some perturbation. Isotopically labeled peptides have been used as standards for the absolute quantification of proteins in complex mixtures. Variations of this approach include the AQUA and SISCAPA methods [7, 8]. Among the advantages of these techniques is that a quantitative assay may be developed for a given protein without the need for an antibody [7]. Alternatively an antibody to a synthetic peptide may be used [8]. This greatly simplifies the development of assays from immunological formats, such as ELISA, where well-characterized antibodies are needed.
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