Genome-wide Proteomics, Chromosome-centric Human Proteome Project (C-HPP), Part II

Paik, Young Ki; Omenn, Gilbert S.; Thongboonkerd, Visith; Markó-Varga, György; Hancock, William S.

doi:10.1021/pr4011958

Cited by 20 publications

(27 citation statements)

References 18 publications

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“…7 Numerous factors have been recognized to account for missing MS evidence of PE2−4 proteins. These factors include: (1) proteins are expressed only in unusual organs or cell types, which can be improved by analyzing the plasma, 10−12 more organs, and cell types; 13−15 (2) proteins are either of low abundance or unsuitable for MS analyses, which can be tackled by improved MS instruments, multiple proteolytic digestion, 16,17 and focusing on subcellular compartments such as detergent-insoluble proteins; 18 and (3) proteins are expressed only in specific or early developmental stages. 19,20 The last problem brought the epigenetic regulation to our attention, as numerous developmental stage specific genes were often switched off due to the DNA−histone association.…”

Section: ■ Introductionmentioning

confidence: 99%

Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria

et al. 2015

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The chromosome-centric human proteome project (C-HPP) has made great progress of finding protein evidence (PE) for missing proteins (PE2-4 proteins defined by the neXtProt), which now becomes an increasingly challenging field. As a majority of samples tested in this field were from adult tissues/cells, the developmental stage specific or relevant proteins could be missed due to biological source availability. We posit that epigenetic interventions may help to partially bypass such a limitation by stimulating the expression of the "silenced" genes in adult cells, leading to the increased chance of finding missing proteins. In this study, we established in vitro human cell models to modify the histone acetylation, demethylation, and methylation with near physiological conditions. With mRNA-seq analysis, we found that histone modifications resulted in overall increases of expressed genes in an even distribution manner across different chromosomes. We identified 64 PE2-4 and six PE5 proteins by MaxQuant (FDR < 1% at both protein and peptide levels) and 44 PE2-4 and 7 PE5 proteins by Mascot (FDR < 1% at peptide level) searches, respectively. However, only 24 PE2-4 and five PE5 proteins in Mascot, and 12 PE2-4 and one PE5 proteins in MaxQuant searches could, respectively, pass our stringently manual spectrum inspections. Collectively, 27 PE2-4 and five PE5 proteins were identified from the epigenetically modified cells; among them, 19 PE2-4 and three PE5 proteins passed FDR < 1% at both peptide and protein levels. Gene ontology analyses revealed that the PE2-4 proteins were significantly involved in development and spermatogenesis, although their chemical-physical features had no statistical difference from the background. In addition, we presented an example of suspicious PE5 peptide spectrum matched with unusual AA substitutions related to post-translational modification. In conclusion, the epigenetically manipulated cell models should be a useful tool for finding missing proteins in C-HPP. The mass spectrometry data have been deposited to the iProx database (accession number: IPX00020200).

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Section: ■ Introductionmentioning

confidence: 99%

Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria

et al. 2015

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“…Using the advanced search interface, users can query using conditional clauses on specific terms and columns. The advanced search can query (1) level of protein evidence (PE), (2) number of known isoforms, (3) number of known variants, (4) number of known post-translational modifications, (5) the presence of disease-related information or not, (6) genes expressed in "body site"/"health state"/"developmental stage" with over/under/exact expression level, (7) protein expression measured by immunohistochemistry in specific "tissues"/"cancers", (8) specific chromosomes, (9) number of peptides depending on annotated type, and (10) range of molecular weights of a protein. …”

Section: Journal Of Proteome Researchmentioning

confidence: 99%

GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project

2015

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Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

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“…1–3 The haploid set of human chromosomes contains 2.9 billion DNA base pairs 4,5 and 20 055 protein-coding genes, according to neXtProt version 2014-09-19. 6 With recent advances in high-throughput mass-spectrometry (MS) and RNaseq technologies, evidence is accumulating that the total number of protein species is much higher than that for genes because of alternative splicing, 7 post-translational modifications, 8 proteolytic modifications, 9 and genetic variations.…”

Section: Introductionmentioning

confidence: 99%

MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome

et al. 2015

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We have developed the web-based Michigan Proteome Visualization Tool (MI-PVT) to visualize and compare protein expression and isoform-level function across human chromosomes and tissues (http://guanlab.ccmb.med.umich.edu/mipvt). As proof of principle, we have populated the tool with Human Proteome Map (HPM) data. We were able to observe many biologically interesting features. From the vantage point of our chromosome 17 team, for example, we found more than 300 proteins from chromosome 17 expressed in each of the 30 tissues and cell types studied, with the highest number of expressed proteins being 685 in testis. Comparisons of expression levels across tissues showed low numbers of proteins expressed in esophagus, but esophagus had 12 cytoskeletal proteins coded on chromosome 17 with very high expression (>1000 spectral counts). This customized MI-PVT should be helpful for biologists to browse and study specific proteins and protein data sets across tissues and chromosomes. Users can upload any data of interest in MI-PVT for visualization. Our aim is to integrate extensive mass-spectrometric proteomic data into the tool to facilitate finding chromosome-centric protein expression and correlation across tissues.

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Genome-wide Proteomics, Chromosome-centric Human Proteome Project (C-HPP), Part II

Cited by 20 publications

References 18 publications

Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria

Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria

GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project

MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome

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