Spanish Human Proteome Project: Dissection of Chromosome 16

Abstract

The Chromosome 16 Consortium forms part of the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a chromosome-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). A Spanish consortium of 16 laboratories was organized into five working groups: Protein/Antibody microarrays, protein expression and Peptide Standard, S/MRM, Protein Sequencing, Bioinformatics and Clinical healthcare, and Biobanking. The project is conceived on a multicenter configuration, assuming the standards and integration procedures already available in ProteoRed-ISCIII, which is encompassed within HUPO initiatives. The products of the 870 protein coding genes in chromosome 16 were analyzed in Jurkat T lymphocyte cells, MCF-7 epithelial cells, and the CCD18 fibroblast cell line as it is theoretically expected that most chromosome 16 protein coding genes are expressed in at least one of these. The transcriptome and proteome of these cell lines was studied using gene expression microarray and shotgun proteomics approaches, indicating an ample coverage of chromosome 16. With regard to the B/D section, the main research areas have been adopted and a biobanking initiative has been designed to optimize methods for sample collection, management, and storage under normalized conditions and to define QC standards. The general strategy of the Chr-16 HPP and the current state of the different initiatives are discussed.

LymPHOS 2.0: an update of a phosphosite database of primary human T cells

“…HPP efforts are distributed among the different partners on a chromosome per partner basis. In this context, LymPHOS data is being integrated on the HPP project through the Spanish Consortia which is in charge of the mining of chromosome 16 ( 21 , 22 ). LymPHOS data contributes both to the description of new modification sites and of the proteome of a primary cell.…”

Multicenter experiment for quality control of peptide-centric LC–MS/MS analysis — A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers

“…The ProteoRed-ISCII consortium has engaged in the Chromosome-centric Human Proteome Project (C-HPP), focusing on the characterization of Chromosome 16 (spHPP) [33,34]. In this context, the present study provided the consortium laboratories with the opportunity to evaluate their performance, and identify strengths and weaknesses in their platform.…”

Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis

“…Switching criteria were set to ions greater than mass to charge ratio (m/z) 350 and smaller than m/z 1,250 with the charge state of 2–5 and an abundance threshold of more than 90 counts (cps). Former target ions were excluded for 15 s. IDA rolling collision energy (CE) parameters script was used for automatically controlling the CE (Segura et al, 2013).…”