Quantitative analysis with mass spectrometric detection is no longer limited to small molecules. A new focus of research is to understand biological processes at the molecular level and this requires more quantitative data for a large range of biomolecules, including low molecular weight compounds, peptides and proteins. On-line approaches such as liquid chromatography (LC) mass spectrometry are restricted to atmospheric pressure ionization (API) in combination with LC while off-line approaches can be performed either with API or matrix assisted laser desorption ionization (MALDI). Selected reaction monitoring quantitation remains the favorite mode of detection for small molecules as well as for proteins and peptides. The potential of quantitative analysis without any chromatographic separation based on chip-based infusion or MALDI has been demonstrated. For the quantitation of small molecules, the use of an internal standard (IS) is well established with structural or isotopically labeled analogs. For proteins, the use of an IS remains more challenging and will need some further optimization. New ionization techniques, such as desorption electrospray ionization, may also open up some new opportunities for quantitative analysis.