We utilise negative controls and replicates to remove unwanted variation and enhance biological signal, outperforming existing methods. Replicates are run on six mass spectrometers operating continuously with varying maintenance schedules over four months, interspersed with ~5000 other runs. We perform 1560 data independent acquisition (DIA)-MS runs of eight samples containing known proportions of ovarian and prostate cancer tissue and yeast, or control HEK293T cells. To enable the deployment of large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time and across instruments and develop computational methods for improving quantitative accuracy.
Reproducible research is the bedrock of experimental science. Nature Communications volume 11, Article number: 3793 ( 2020) Strategies to enable large-scale proteomics for reproducible research
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