Table 1.
Challenges associated with different aspects of quantitative mass spectrometry.
| aspect | challenge |
|---|---|
| sample preparation | sample purification or fractionation can reduce sample matrix interferences. Sample concentration and dilution can bring the analytes to the working range of the mass spectrometric method. However, these steps limit sample throughput |
| sample homogeneity | inhomogeneous samples are not amenable to quantitative analysis. Thus, analysis of dry sample/matrix deposits by MALDI-MS proves to be cumbersome |
| labelling | there is a limited range of chemical labels (derivatizing agents) for the target molecules of interest |
| internal standards | in many cases, it is difficult to find the right internal standards with similar ionization efficiencies to those of the analytes. Sometimes, isotopologues of analytes need to be synthesized for use as internal standards |
| interfacing | samples in the solid phase or liquid phase need to be brought to the gas phase, typically before or during ionization of analyte molecules |
| ion suppression | sample matrix components suppress ionization of different analytes to a different extent. The extent of ion suppression may change depending on the operating conditions |
| separation | separation of analytes by liquid or gas chromatography, capillary electrophoresis, ion mobility spectroscopy, or other techniques can reduce sample matrix interferences but it complicates analytical workflows, and (usually) limits sample throughput |
| detection | detection efficiencies for ions with different m/z values are unequal |
| spectral interferences | some sample matrix and/or ionization matrix-derived ions may overlap with the analyte ions |
| concentration/mass calibration | signal–quantity dependencies are not linear over a broad range. Parameters of the calibration equations may drift over time |
| automation | automated sample handling equipment can improve repeatability but it is costly |
| data processing and interpretation | expert knowledge is needed to translate the bare data acquired by a mass spectrometer into useable results, and finally—scientifically sound conclusions |