A draft map of the human proteome

Abstract

The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides does not exist yet. Here, we present a draft map of the human proteome using high resolution Fourier transform mass spectrometry. In-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells resulted in identification of proteins encoded by 17,294 genes accounting for ~84% of the total annotated protein-coding genes in humans. A unique and comprehensive strategy for proteogenomic analysis enabled us to discover a number of novel protein-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream ORFs. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) will complement available human genome and transcriptome data to accelerate biomedical research in health and disease.

The human RBPome: From genes and proteins to human disease

“…We examined the expression patterns of the RBP catalogue across 17 adult tissues and 6 hematopoietic cells from the recently published human proteome catalogue [24]. Further, tissue specificity of the expression pattern was estimated using an index that varies between zero (for housekeeping genes) and one (observed for tissue specific genes) [25,26].…”

“…We examined the expression patterns of RBPs across 17 adult tissues and 6 hematopoietic cells from recently published human proteome catalogue [24]. A complete linkage hierarchical clustering of the expression levels ( Figure 4A) groups tissues exhibiting similar levels of expression.…”

GWIPS‐viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms

“…Phylogenetic evidence also strongly supports the functional importance of this uORF product in addition to the uORF's regulatory role in providing stress resistance to the translation of the annotated CDS 45. The detection of a product translated from an ORF in the 3′UTR of the human CHTF8 gene has also been reported 43, 44. Indeed in GWIPS‐viz, a high ribosome occupancy can be seen in the 3′UTR region of the human CHTF8 transcripts (Fig.…”

Exploring the potential of public proteomics data

“…Several such generic repositories are now available, for example PRIDE 4, GPMDB 5, PeptideAtlas 6, and MassIVE (http://massive.ucsd.edu/ProteoSAFe) for shotgun results; and PASSEL 7, SRMAtlas (http://www.srmatlas.org), and Panorama 8 for targeted proteomics quantification data. More specific databases have also been established, related to: diseases, for example TBDB for tuberculosis 9; organisms, for example ProteomicsDB 10 and the Human Proteome Map 11 for the human proteome, and pep2pro for Arabidopsis 12; or subproteomes, for example CSF‐PR 13 for cerebrospinal fluid or TOPPR 14 and TopFIND 15 for in vivo cleaved proteins. For a comprehensive overview of the current proteomics databases and repositories, please see Perez‐Riverol et al 16.…”

“…More recently, there is an ongoing debate about the two drafts of the human proteome published in Nature in 2014 10, 11. Both studies provided an exemplary precedent by sharing all generated data (available as datasets PXD000561 and PXD000865 in PRIDE).…”