Automatic Quality Assessment Of Mass Spectrometry Experiments By Multivariate Quality Control Metrics

Wout Bittremieux, Pieter Meysman, Lennart Martens, Dirk Valkenborg, Kris Laukens
2016 Zenodo  
Automatic quality assessment of mass spectrometry experiments by multivariate quality control metrics and the relation between low-quality experiments and identifications Introduction Despite the many recent technological and computational advances, performing a mass spectrometry experiment remains a complex activity and its results are subject to a large variability. To understand and evaluate how technical variability affects an experiment, several computationally derived quality control (QC)
more » ... metrics have been introduced. However, despite the availability of QC metrics covering a wide range of qualitative information, a systematic approach to quality control is often still lacking. We will illustrate how QC metrics can be used to automatically discriminate between low-quality and high-quality experiments. A special emphasis will be laid on the interpretability of the results, as in order to systematically integrate QC practices into existing workflows, interpretability of the qualitative information is paramount. Methods We use unsupervised outlier detection based on identification-free QC metrics to detect deviating experiments with a low performance. By identifying outliers based on their local neighborhood we are able to directly apply our technique to data acquired on different instrument types. Furthermore, it is insufficient to only know that an experiment is an outlier, it is also of vital importance to know why. To explain why an experiment is an outlier, the subspace of QC metrics in which it can be differentiated from the other experiments is identified, which aids the interpretation of the low-quality experiments. Furthermore, the subspaces for the low-quality experiments can be used to discover which QC metrics have an influence on the identification performance. Preliminary Data or Plenary Speakers Abstract We used a public dataset of standard QC LC-MS runs performed on different instruments at the Pacific Northwest Nation [...]
doi:10.5281/zenodo.55998 fatcat:267h2ytb5jdybitxdljea2e2a4