This dataset is included as one of the benchmarking dataset in the manuscript "msBayesImpute: A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data" by He et al (https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1). To better recapture the missing value pattern in a real-world situation, the missing values were experimentally introduced through mass-spectrometry measurements of lysates of 20 paired tumour/tumour-free tissues from 10 lung cancer patients without dilution and with dilution fractions of 75% and 50%.