PeptideAtlas and the Chromosome-Centric Human Proteome Project (C-HPP)

In 2010, the Chromosome-centric Human Proteome Project (C-HPP) was launched as a component of the Human Proteome Project (HPP) with the initial goal of characterizing a single protein form for each currently identified protein-coding gene. The Human PeptideAtlas builds are an essential resource for the project, combining data from over 1000 experiments, covering a wide variety of sample types, all processed through a uniform computational pipeline to yield a final protein list with a stringent, less than 1% FDR (false discovery rate).

Download

2025 Latest

HPP Reference Proteome Table [5.1MB]
HPP Reference Proteome FASTA file [7.5MB]
Common contaminants FASTA file [116kB]

PeptideAtlas vs C-HPP Summary Table

PeptideAtlas Builds:

Column descriptions:

coreProteome Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold