Figure 1. Experimental design and data representation of the proteomics study of lung tissues from GTEx.

(A) TMT10plex labeling was used to profile peptides from lung specimens (${\mathrm{S}}_1,\dots ,{\mathrm{S}}_8$) and two references (Q: lung-specific reference, ${\mathrm{S}}_0$: mega-pool) across 36 blocks. Each specimen was analyzed in two blocks; ${\mathrm{S}}_2$ in Blocks 1 and R illustrates replicates. (B) TMT-LC-MS platform generated spectra for protein identification and quantification. (C) Protein abundance $Y_{gk}$ is defined as the log₂ ratio of sample intensity to the tissue-specific reference (Q) in the same block and serves as input for both PQN and ProMix.