ABSTRACT The advantages of combining qualitative and quantitative analysis on a single analytical technique have further extended the applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to the quantitation of various biomolecules. To achieve absolute quantitation, it is necessary to perform a calibration with standard dilutions. For the purpose of measuring DNA samples, a pure DNA oligonucleotide at different concentrations was chosen as a standard to perform the calibration of MALDI-TOF MS. In order to overcome the variation of signal intensity from repeated measurements of each DNA standard dilution, fixed amount of an internal standard was added into each DNA standard dilution. Instead of maintaining at a constant level, the signals of fixed amount of internal standard were decreased 73% from its initial level while the signals of DNA standard continued to increase within a linear dynamic range for quantitation from 0.20 μM to 12.5 μM of DNA. Attempts to identify the cause of signal reduction were systematically carried out. This is the first report on the extent of signal reduction in quantitative MALDI-TOF MS. These results represent a limitation on using MALDI-TOF MS to monitor the changes in concentration of two different compounds within a chemical or biological system.
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