Advances in MALDI mass spectrometry in clinical diagnostic applications

Abstract

The concept of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was first reported in 1985. Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. These technologies are high-throughput and sensitive. Emerging evidence has shown that they are not only useful in qualitative and quantitative analyses of proteins, but also of other types of biomolecules, such as DNA, glycans, and metabolites. Recently, parallel fragmentation monitoring (PFM), which is a method comparable to selected reaction monitoring, has been reported. This highlights the potentials of MALDI-TOF/TOF tandem MS in quantification of metabolites. Here we critically review the applications of the major MALDI MS technologies, including MALDI-TOF MS, MALDI-TOF/TOF MS, SALDI-TOF MS, MALDI-QqQ MS, and SELDI-TOF MS, to the discovery and quantification of disease biomarkers in biological specimens, especially those in plasma/serum specimens. Using SELDI-TOF MS as an example, the presence of systemic bias in biomarker discovery studies employing MALDI-TOF MS and its possible solutions are also discussed in this chapter. The concepts of MALDI, SALDI, SELDI, and PFM are complementary to each other. Theoretically, all these technologies can be combined, leading to the next generation of the MALDI MS technologies. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming.

Fig. 1

A typical workflow of sample spot preparations for analyses by MALDI-TOF MS and SALDI-TOF MS. In conventional MALDI-TOF MS, the analytes and chemical matrix are mixed and dried to form co-crystals, whereas analytes are coated homogeneously and distributed evenly on a layer of solid matrix in SALDI-TOF MS

Fig. 2

(a) A typical workflow of quantitative profiling of N-linked glycans carried by proteins in whole serum (steps 1 and 3–5) or N-linked glycans carried by a single serum protein (steps 1–5) by MALDI-TOF MS. (b) Representative quantitative N-glycan profile from transferrin purified from serum by micro-scale antibody affinity chromatography. (c) Representative quantitative N-glycan profile from proteins in whole serum

Fig. 3

Representative MALDI-TOF/TOF tandem MS spectra of citrulline (a) and [ureido-¹³C] citrulline (b) acquired independently with graphene flake as the solid matrix. (c) Representative linear calibration curve of the PFM assay for quantitative analysis of citrulline in the range of 10–250 μM. The peak intensity ratios of the indicator fragment ion of citrulline (m/z 153.1) to that of [ureido-¹³C] citrulline (m/z 154.1) in the calibration standards were plotted against the citrulline concentrations

Fig. 4

(a) Typical workflow of quantitative proteomic profiling by SELDI-TOF MS. After denaturation and dilution, a patient sample is added to a binding surface of a ProteinChip array. (b) After incubation and washing, proteins with matched physicochemical/biochemical properties are retained on the surface. (c) Then a chemical matrix is added. (d) After drying, the sample spot is subjected to MALDI-TOF MS analysis to obtain signals from various positions with a regular spacing (e) (dark circles) throughout the entire spot. (f) After summing up the MS signals, a quantitative proteomic profile is obtained

Fig. 5

The study designs which were used to identify biomarkers for diagnosis of SARS in adults (a) and diagnosis of necrotizing enterocolitis/late-onset sepsis in preterm infants (b) by undertaking MS-based proteomic profiling approaches. In the SARS study, potential diagnostic SELDI peaks were filtered by only considering those that were significantly correlated with at least two disease-associated biochemical/clinical parameters as SARS-specific (a) [99]. In the preterm infant study, the longitudinal samples were used to verify the clinical relevance of the differential proteomic features [25]. Only the differential MS peaks showing statistically significant reverse of peak intensities upon recovery were retained (b). In both studies, about 80% of differential SELDI peaks, which were obtained by case–control comparison, were rejected