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Search HPP Proteomics data in UniProt

Source: R/uniprot_proteomics.R
rba_uniprot_proteomics_hpp_search.Rd

Search for Human Proteome Project (HPP) proteomics features mapped to UniProt proteins. Refine the search by data source, peptide, or other supported criteria.

Usage

rba_uniprot_proteomics_hpp_search(
  accession = NULL,
  taxid = NULL,
  data_source = NULL,
  upid = NULL,
  peptide = NULL,
  unique = NULL,
  ...
)

Arguments

accession

Character: (optional) UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

taxid

Numeric: (optional) NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

data_source

Character: (optional) Proteomics data source. You can supply up to two values. Use rba_uniprot_proteomics_species() to retrieve the sources currently available for each species and category.

upid

Character: (optional) UniProt Proteome identifier (UPID). You can supply up to 100 UPIDs.

peptide

Character: (optional) Peptide sequence(s). You can supply up to 20 sequences.

unique

Logical: (optional) Filter by peptide uniqueness. If TRUE, return peptides mapping to one protein; if FALSE, return non-unique peptides; if NULL, do not apply this filter.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list in which each element corresponds to a UniProt protein and proteomics data are stored under the features element.

Details

At least one of accession, taxid, data_source, upid, or peptide is required. unique only refines those criteria.

UniProt categorizes proteomics data sources into three main data categories: PTM (Post-Translational Modification), non-PTM, and HPP (Human Proteome Project); each with corresponding API endpoints, and thus, rbioapi functions.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/proteomics/hpp"

References

  • The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010

  • Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237

  • Proteins API Documentation

  • Citations note on UniProt website

See also

Other "UniProt - Proteomics": rba_uniprot_proteomics_hpp(), rba_uniprot_proteomics_non_ptm(), rba_uniprot_proteomics_non_ptm_search(), rba_uniprot_proteomics_ptm(), rba_uniprot_proteomics_ptm_search(), rba_uniprot_proteomics_species()

Examples

# \donttest{
  rba_uniprot_proteomics_hpp_search(peptide = "NDQVYQPLRDRDDAQYSHLGGNWAR")
# }