Observations from the proteomics bench

Many challenges in proteomics result from the high-throughput nature of the experiments. The paper first presents pre-analytical problems, which still occur, although the call for standardisation in omics has been ongoing for many years. This article also discusses aspects, which affect bioinformatic analysis, based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data set-wise quality control is still necessary and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations.