Biomarkers sample quality controls

The effects of the appropriate environmental matrices (soil, water, air, biological - for biomarker or exposure assessment studies) on assay performance must be well characterized and documented. The SOP must also include the degree of quality control necessary to ensure the satisfactory performance of the method. Quality control procedures must address the required sample preparation steps, reagent stability, instrumentation, data handling and analysis. In many immunoassay SOPs that the EPA has reviewed, quality control is totally lacking or minimally addressed particularly for the sample preparations. The Agency can provide direction on what is an appropriate degree of quality control based on the objective of the method. 

In-study validation entails the routine monitoring of the quality control samples to determine whether the analytical method is performing consistently over time and whether data from a particular plate or run are acceptable. In addition, especially for biomarker assays, evaluation of parallelism using incurred samples is carried out to confirm the validity and suitability of the reference standard. 

Encouraged by this spectral reproducibility, we focused our efforts on the particularly challenging problem of distinguishing bacterial strains by MALDI MS. We developed a modified correlation approach22 that relies on two fundamental qualities of bacterial mass spectra. First, because different bacterial strains of the same species have substantial, if not complete, genetic overlap, most of the protein masses observed with two different strains will be identical. This feature limits the value of the biomarker approach that is commonly used to differentiate bacteria species. Second, as just noted, closely controlled sample preparation and mass analysis procedures can result in highly reproducible results.22 The modified correlation approach takes advantage of subtle, yet reproducible, differences in mass spectra obtained from dif-... 

The sample preparation methods and the separation techniques have to be developed carefully in order to facilitate the entire biomarker discovery process. Sample preparation methods should be compatible with the subsequent steps in the sample preparation process. The use of a sample preparation method that results in the sample being in a solution that is incompatible with the separation method to be used will cause problems such as increased experimental difficulty, sample loss, increased time, and experimental cost. A good sample preparation method will facilitate quality results and the collection of good data. Good-quality results are easier to analyze and less prone to experimental errors that require high numbers of replicates to control. 

---