For samples that will be directly compared to each other, sample preparation and measurements should be performed at the same time. This optimizes the amount of information collected for each assay and measures molecules of interest using the same conditions.
Two examples of experimental design (dose-response and temporal) recommendations in regard to minimum controls and biological replicates for mass spectrometry analysis are shown below.
In addition, for each project CIT staff pools together samples used for quality control (equal volume amounts of each sample) and injects these for analysis prior to and after every 10 individual sample injections. These quality control samples are used to assess instrument variability, data quality and injection volume variations. The number of required technical replicates will vary based on experimental design to ensure data quality is high and variations in samples owing to instrumentation variation is minimized.