The objective of this work is the development of quantitative methods, based on LC-MS, targeting small intracellular metabolites in yeast and yeast derived products. Development covers all aspects from sample preparation to detection by complementary separation and mass spectrometric detection systems. The first presented method is dedicated to the quantification of nucleotides, nucleosides and nucleobases by LC-MS/MS. Excellent separation of these analytes was found using a reversed phase material. Comparison with other separations revealed superior separation efficiency and lower limits of detection. Employment of ESI-triple quadrupole MS enabled selective and interference-free detection. The quantitative method was applied in nucleotide enriched yeast autolysates and it was validated by use of a complementary nucleotide detection via inductively coupled plasma MS. The second presented method deals with quantitative metabolite profiling of living yeast cells from the bioreactor. Fast sampling, the arrest of metabolic activity, efficient cell extraction and the avoidance or compensation of any losses were the main challenges here for accurate quantification. The established sample preparation, which was optimized for the yeast Pichia pastoris fulfills all requirements. The multitarget analysis of a wide range of intracellular metabolites was carried out via LC-MS/MS employing reversed phase LC, HILIC and triple quadrupole MS. Furthermore, a fully 13C labeled yeast extract was produced and its suitability as internal standard was evaluated. Within this work, this labeled cell extract was used as a tool to evaluate the recoveries and repeatability precisions of the cell extraction and the extract treatment. Finally the total combined uncertainties of the sample preparation procedure for yeast could be estimated using a model equation for uncertainty budgeting and error propagation for all input variables.