Dataset of Rat and Human Serum Proteomes Derived from Differential Depletion Strategies prior to Mass Spectrometry

This article provides information regarding the effect of four common high abundant protein (albumin and immunoglobulins (Ig)) depletion strategies upon serum proteomics datasets derived from normal, non-diseased rat or human serum. After tryptic digest, peptides were separated using C₁₈ reverse phase liquid chromatography-tandem mass spectrometry (rpLC-MS/MS). Peptide spectral matching (PSM) and database searching was conducted using MS Amanda 2.0 and Sequest HT. Peptide and protein false discovery rates (FDR) were set at 0.01%, with at least two peptides assigned per protein. Protein quantitation and the extent of albumin and Ig removal was defined by PSM counts. Venn diagram analysis of the core proteomes, derived from proteins identified by both search engines, was performed using Venny. Ontological characterization and gene set enrichment were performed using WebGestalt. The dataset resulting from each depletion column is provided.