Published July 26, 2017 | Version v1
Journal article Open

Quality control in mass spectrometry-based proteomics

  • 1. University of Antwerp
  • 2. Stellenbosch University
  • 3. Ghent University


Mass spectrometry is a highly complex analytical technique and mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining accurate and reproducible results. Therefore, a comprehensive and systematic approach to quality control is an essential requirement to inspire confidence in the generated results.
A typical mass spectrometry experiment consists of multiple different phases including the sample preparation, liquid chromatography, mass spectrometry, and bioinformatics stages. We review potential sources of variability that can impact the results of a mass spectrometry experiment occurring in all of these steps, and we discuss how to monitor and remedy the negative influences on the experimental results. Furthermore, we describe how specialized quality control samples of varying sample complexity can be incorporated into the experimental workflow and how they can be used to rigorously assess detailed aspects of the instrument performance.

This is the peer reviewed version of the following article: "Bittremieux, W., Tabb, D. L., Impens, F., Staes, A., Timmerman, E., Martens, L. & Laukens, K. Quality control in mass spectrometry-based proteomics. Mass Spectrometry Reviews (2017)", which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.


Bittremieux_2017_Quality control in mass spectrometry-based proteomics.pdf