Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically falls behind learning new techniques, instruments, or software. Considering how important QC is in a core setting where data is generated for non-mass spectrometry experts and confidence in delivered results is paramount, we have created this quick-start guide focusing on off-the-shelf QC materials and relatively easy to use QC software. We hope that by providing a background on the different levels of QC, different materials and their uses, describing QC design options, and highlighting some current QC software, that implementing QC in a core setting will be easier than ever. There continues to be development in each of these areas (such as new materials and software), and the current generation of QC mass spectrometry-based proteomics is more than capable of conveying confidence in results as well as minimizing laboratory downtime by guiding experimental, technical, and analytical troubleshooting from sample to results.