Dataset Information

Human spermatozoa as a model for detecting missing proteins in the context of the chromosome-centric Human Proteome Project.

ABSTRACT: Data from ProteomeXchange, PXD ID: PXD002367. File: Mitchell_40_F03_exclu02.mzml. Published as part of J Proteome Res. 2015 . From the Abstract: {{i}} The chromosome-centric Human Proteome Project (C-HPP) aims at cataloguing the proteins as gene products encoded by the human genome, in a chromosome-centric manner. The existence of products of about 82% of the genes has been confirmed at the protein level. However, the number of so-called missing proteins remains significant. It was recently suggested that the expression of proteins that have been systematically missed might be restricted to particular organs or cell types, for example the testis. Testicular function, and spermatogenesis in particular, is conditioned by the successive activation and/or repression of thousands of genes and proteins, including numerous germ cell- and testis-specific products. Both the testis and post-meiotic germ cells are thus promising sites at which to search for missing proteins and ejaculated spermatozoa are a potential source of proteins whose expression is restricted to the germ cell lineage. A trans-chromosome-based data analysis was performed to catalog missing proteins in total protein extracts from isolated human spermatozoa ... {{/i}}

INSTRUMENT(S): Instrument

ORGANISM(S): Homo_sapiens_viruses, Human

DISEASE(S): Not Available

SUBMITTER: Jumeau F, et al.

PROVIDER: GPM32320016359 | GPMDB |

REPOSITORIES: GPMDB

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Publications

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project.

Jumeau Fanny F Com Emmanuelle E Lane Lydie L Duek Paula P Lagarrigue Mélanie M Lavigne Régis R Guillot Laëtitia L Rondel Karine K Gateau Alain A Melaine Nathalie N Guével Blandine B Sergeant Nicolas N Mitchell Valérie V Pineau Charles C

Journal of proteome research 20150730 9

The Chromosome-Centric Human Proteome Project (C-HPP) aims at cataloguing the proteins as gene products encoded by the human genome in a chromosome-centric manner. The existence of products of about 82% of the genes has been confirmed at the protein level. However, the number of so-called "missing proteins" remains significant. It was recently suggested that the expression of proteins that have been systematically missed might be restricted to particular organs or cell types, for example, the te ...[more]

PMID: 26168773

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Project description:Human umbilical vein endothelial cells (HUVECs) are a widely-used model system to study pathological and physiological processes associated with the cardiovascular system. An understanding of genes and proteins that are expressed in any cell type is a fundamental need which facilitates studies of molecular changes in disease states and response to various stimuli. In this study, we employed next generation sequencing and mass spectrometry to profile the transcriptome and proteome of primary HUVECs. Analysis of 145 million paired-end reads from next generation sequencing confirmed expression of 12,186 protein-coding genes (FPKM>0.1), 439 novel long non-coding RNAs and revealed 6,089 novel isoforms that were not annotated in GENCODE. A comparison of the transcripts against human gene expression data for 53 tissues catalogued by the Genotype-Tissue Expression (GTEx) project revealed a number of HUVEC-specific genes. Proteomics analysis identified 6,477 proteins including confirmation of N-termini for 1,091 proteins and isoforms for 149 proteins for which transcriptomic evidence was observed. Alternate translational start sites for seven proteins and alternate splicing in five proteins were also identified. A database search to specifically identify other post-translational modifications provided evidence for a number of modification sites on 117 proteins which included ubiquitylation, lysine acetylation and mono, di- and tri-methylation events. Based on the data from this study and a survey of other databases, we provide evidence for 11 “missing proteins,” which are proteins for which there was insufficient or no protein level evidence. Peptides supporting missing protein and novel events were validated by comparison of MS/MS fragmentation patterns with synthetic peptides. By creating a custom database of proteins containing sample-specific single amino acid variants (SAAV), we also identified 245 variant peptides derived from 207 expressed proteins. Overall, we believe that the integrated approach employed in this study is widely applicable to study any primary cell type for deeper molecular characterization.

Dataset Information

Human spermatozoa as a model for detecting missing proteins in the context of the chromosome-centric Human Proteome Project.

Publications

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project.

Similar Datasets

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