Integrated View of Baseline Protein Expression in Human Tissues

Prakash, Ananth, Garcia-Seisdedos, David, Wang, Shengbo, Kundu, Deepti Jaiswal, Collins, Andrew ORCID: 0000-0003-0507-6912, George, Nancy, Moreno, Pablo, Papatheodorou, Irene, Jones, Andrew R ORCID: 0000-0001-6118-9327 and Vizcaino, Juan Antonio (2023) Integrated View of Baseline Protein Expression in Human Tissues. JOURNAL OF PROTEOME RESEARCH, 22 (3). pp. 729-742.

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Official URL: http://dx.doi.org/10.1021/acs.jproteome.2c00406

Abstract

The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.

Item Type:	Article
Uncontrolled Keywords:	mass spectrometry, quantitative proteomics, public data re-use, human proteome
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	08 Feb 2023 14:49
Last Modified:	28 Apr 2023 13:05
DOI:	10.1021/acs.jproteome.2c00406
Open Access URL:	https://doi.org/10.1021/acs.jproteome.2c00406
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3168271