Identification of Missing Proteins in the neXtProt Database and Unregistered Phosphopeptides in the PhosphoSitePlus Database As Part of the Chromosome-Centric Human Proteome Project

The Chromosome-Centric Human Proteome Project (C-HPP) is an international
effort for creating an annotated proteomic catalog for each chromosome.
The first step of the C-HPP project is to find evidence of expression
of all proteins encoded on each chromosome. C-HPP also prioritizes
particular protein subsets, such as those with post-translational
modifications (PTMs) and those found in low abundance. As participants
in C-HPP, we integrated proteomic and phosphoproteomic analysis results
from chromosome-independent biomarker discovery research to create
a chromosome-based list of proteins and phosphorylation sites. Data
were integrated from five independent colorectal cancer (CRC) samples
(three types of clinical tissue and two types of cell lines) and lead
to the identification of 11,278 proteins, including 8,305 phosphoproteins
and 28,205 phosphorylation sites; all of these were categorized on
a chromosome-by-chromosome basis. In total, 3,033 “missing
proteins”, i.e., proteins that currently lack evidence by mass
spectrometry, in the neXtProt database and 12,852 unknown phosphorylation
sites not registered in the PhosphoSitePlus database were identified.
Our in-depth phosphoproteomic study represents a significant contribution
to C-HPP. The mass spectrometry proteomics data have been deposited
to the ProteomeXchange Consortium with the data set identifier PXD000089