2 research outputs found
neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
About 5000 (25%) of the âŒ20400 human protein-coding
genes
currently lack any experimental evidence at the protein level. For
many others, there is only little information relative to their abundance,
distribution, subcellular localization, interactions, or cellular
functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org) is to collect this information for every human protein. HPP is
based on three major pillars: mass spectrometry (MS), antibody/affinity
capture reagents (Ab), and bioinformatics-driven knowledge base (KB).
To meet this objective, the Chromosome-Centric Human Proteome Project
(C-HPP) proposes to build this catalog chromosome-by-chromosome (www.c-hpp.org) by focusing primarily on proteins that currently
lack MS evidence or Ab detection. These are termed âmissing
proteinsâ by the HPP consortium. The lack of observation of
a protein can be due to various factors including incorrect and incomplete
gene annotation, low or restricted expression, or instability. neXtProt
(www.nextprot.org) is a new web-based knowledge platform
specific for human proteins that aims to complement UniProtKB/Swiss-Prot
(www.uniprot.org) with detailed information obtained from
carefully selected high-throughput experiments on genomic variation,
post-translational modifications, as well as protein expression in
tissues and cells. This article describes how neXtProt contributes
to prioritize C-HPP efforts and integrates C-HPP results with other
research efforts to create a complete human proteome catalog
Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project
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 âmissing
proteinsâ 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 or repression of thousands
of genes and proteins including numerous germ cell- and testis-specific
products. Both the testis and postmeiotic 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. We have identified and manually validated
peptide matches to 89 missing proteins in human spermatozoa. In addition,
we carefully validated three proteins that were scored as uncertain
in the latest neXtProt release (09.19.2014). A focus was then given
to the 12 missing proteins encoded on chromosomes 2 and 14, some of
which may putatively play roles in ciliation and flagellum mechanistics. The expression pattern of C2orf57
and TEX37 was confirmed in the adult testis by immunohistochemistry.
On the basis of transcript expression during human spermatogenesis,
we further consider the potential for discovering additional missing
proteins in the testicular postmeiotic germ cell lineage and in ejaculated
spermatozoa. This project was conducted as part of the C-HPP initiatives
on chromosomes 14 (France) and 2 (Switzerland). The mass spectrometry
proteomics data have been deposited with the ProteomeXchange Consortium
under the data set identifier PXD002367