neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects

Abstract

About 5000 (25%) of the ~20400 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 "missing proteins" 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.

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines

“…They include GPMDB [12], MOPED [13], ProteomicsDB [14], MaxQB [15], and Human Proteome Map [16]. In addition, other databases whose primary focus is perhaps not exclusively on proteomics may also contain information on protein abundances, notably UniProt [17] and NextProt [18].…”

Proteomic profiling of nipple aspirate fluid (NAF): Exploring the complementarity of different peptide fractionation strategies

“…Although we applied stringent data filters in a two-step process using a Bayesian discriminator [23] and searched against neXtProt database (DB) [manually annotated and recommended by HUPO (Human Proteome Organization)] [32], the number of identified proteins was relatively low for this complex mixture [8,19]. The three most widely adopted strategies for improving HPLC separation (quantified by the peak capacity parameter, i.e., the maximum number of components that can be resolved in a given separation time) are: increasing the column length, using shallow gradients (proportionally increasing gradient time) and reducing the packing material particle size.…”

Structural Bioinformatics Analysis On Diabetes Associated Proteins

“…Soluble IAPP oligomers have been exhibited to be cytotoxic and possibly responsible for beta cell apoptosis in T2DM. In addition, beta cells with a high replication rate have been observed to be more susceptible to apoptosis by IAPP oligomers [63]. There is the precision balance between refolding and degradation, kept by the quality control system that shows the amount of mutant protein allowed to accumulate.…”