Why Reproducible Outcomes are Essential in Proteomic Research and Why Standardisation of Processes is Essential for Achieving Reproducibility

摘要

In both 2D electrophoresis and LC-MS proteomic analysis we are dealing with highly complex samples, and there are many complex processes involved which in turn can be affected by a host of parameters and issues such as reagent batches, column performance, even the temperature of the lab. This complexity means that it can be very difficult to generate the same results from the same samples in different labs and even in the same lab at different times. This in turn makes it very difficult for labs to build upon published results, a fundamental principle of the scientific method. Quality Control (QC), based on the use of standards to monitor levels of technical variation in industrial processes is fundamental in the output of a reproducible product. We argue that because proteomic analysis is significantly more challenging than most industrial processes, employing standards and the standardisation of processes in proteomics experiments is key to arriving at reproducible outcomes. Focusing mainly on 2D electrophoresis and to some extent on LC-MS we examine the importance of standardisation and how such standards may be applied to Proteomic research in order to facilitate reproducible discoveries. Using studies carried out with single and multi-users from within and between different laboratories, we describe our experiences of achieving standardisation using Standard samples to provide feedback on the reproducibility of each stage and as well as the complete proteomic workflow.