spike-in label free DIA proteome

This is a mixed complex (“three proteome”) dataset specifically for evaluation of DEqMS. Briefly, <i>E. coli</i> and <i>C. elegans</i> extracted proteomes were spiked into an <i>H. sapiens</i> proteome (HeLa cells) at ratio <i>E. coli</i>: <i>C. elegans</i>: <i>H. sapiens</i> equal to 2:1:7 (group A) or 1:2:7 (group B). The samples were prepared in triplicates, with each sample containing 100 µg of protein in total. The digested peptide mixtures were analyzed by Orbitrap Fusion with FAIMS Pro using DIA acquisition method. The data was searched by Spectronaut via direct-DIA mode using a combined protein database including <i>H. sapiens</i>, <i>E. coli</i>, and <i>C. elegans</i> proteome sequences downloaded from Uniprot. MS raw data has been uploaded to ProteomeXchange with identifier PXD038624.