Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets

• DOI: 10.1021/acs.jproteome.4c00788
• Publication Date: 2025-01-07T09:47:59Z
• Authors: Ananth Prakash; Andrew Collins; Liora Vilmovsky; Silvie Fexova; Andrew R. Jones; Juan Antonio Vizc...

AbstractThe PRIDE database is the largest public data repository of mass spectrometry-based proteomics data and currently stores more than 40,000 datasets covering a wide range of organisms, experimental techniques and biological conditions. During the past few years, PRIDE has seen a significant increase in the amount of submitted Data-Independent Acquisition (DIA) proteomics datasets. This provides an excellent opportunity for large scale data reanalysis and reuse.We have reanalysed 15 public label-free DIA datasets across various healthy human tissues, to provide a state-of-the-art view of the human proteome in baseline conditions (without any perturbations). We computed baseline protein abundances and compared them across various tissues, samples and datasets. Our second aim was to compare protein abundances obtained here from the results of previous analyses using human baseline Data-Dependent Acquisition (DDA) datasets. We observed a good correlation across some tissues, especially in liver and colon but weak correlations were found in others, such as lung and pancreas. The reanalysed results including protein abundance values and curated metadata are made available to view and download from the resource Expression Atlas.For TOC Only