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

Abstract

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, 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 for 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.

Keywords: best practices; materials; proteomics; quality control; software; standards.

Figure 1. Four Levels of QC Material. In general, there are 4 types, or levels, of QC materials, described in the Introduction section and in detail throughout. A QC1 material is a mixture of peptides (shown in cyan and red), isotopically labeled or not; a QC2 material is a whole-cell digest or biofluid digest (shown as a green lined “cell” with its components); and a QC3 material is a mix of isotopically labeled peptides mixed into a more complex whole-cell digestor biofluid. Finally, a QC4 material is 2 or more samples of whole-cell lysate or biofluid digests (here, A and B) that have known mixtures of different species’ proteomes (shown as green versus pink cells, at ratios of 2:1 or 1:2). Note that this is only describing types of QC materials, while recommendations for implementing QC in experimental design can be found in the Methods for Implementing QC section.