Proteogenomics Dashboard for the Human Proteome Project

Abstract

dasHPPboard is a novel proteomics-based dashboard that collects and reports the experiments produced by the Spanish Human Proteome Project consortium (SpHPP) and aims to help HPP to map the entire human proteome. We have followed the strategy of analog genomics projects like the Encyclopedia of DNA Elements (ENCODE), which provides a vast amount of data on human cell lines experiments. The dashboard includes results of shotgun and selected reaction monitoring proteomics experiments, post-translational modifications information, as well as proteogenomics studies. We have also processed the transcriptomics data from the ENCODE and Human Body Map (HBM) projects for the identification of specific gene expression patterns in different cell lines and tissues, taking special interest in those genes having little proteomic evidence available (missing proteins). Peptide databases have been built using single nucleotide variants and novel junctions derived from RNA-Seq data that can be used in search engines for sample-specific protein identifications on the same cell lines or tissues. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. The dasHPPboard can be freely accessed at: http://sphppdashboard.cnb.csic.es.

Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence

“…Public data sets from different resources such as the Gene Expression Omnibus (GEO) database 14 and the ENCODE project 15 were analyzed in depth to define the set of expressed genes in thousands of samples, including different biological sources (cell lines, normal tissues, and cancer samples) and technologies (microarrays and RNA-Seq). 16 In addition, a bayesian classifier was developed to score the probability of expression of the missing proteins in more than 3400 microarray experiments. 17 According to this study, testis, brain, and skeletal muscle were the best tissue candidates to detect the higher number of missing proteins using shotgun proteomics.…”

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

“…The “dasHPPboard” developed by the Chromosome 16 group in Spain has facilitated the analysis of a variety of proteogenomic data sets. This tool can be used to identify samples with high amount of transcript for MPs of category PE2 [33]. The Michigan Proteome Visualization Tool (MI-PVT), developed by the Chromosome 17 teams of the US, is a web-based tool that displays by chromosome or by protein family [34].…”

Clinical implications of recent advances in proteogenomics

“…Further evidence for the existence of a given protein may be obtained using in vitro transcription/translation strategies developed to devise precise conditions and parameters that are then applied for the identification of missing proteins in human cells and tissues using targeted mass spectrometry [39]. Last but not least, numerous bioinformatic pipelines or tools have become available to assist this inventory of missing proteins or splice variants by proteogenomics [40][41][42][43][44][45][46], while metrics for high confidence identification of "missing" proteins are just emerging [47]. Besides the common core proteome, more specific sets of proteins with highly variable sequences require dedicated efforts.…”