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Search HPP Proteomics data in UniProt

Source: R/uniprot_proteomics.R
rba_uniprot_proteomics_hpp_search.Rd

Using this function, you can search for HPP (Human Proteome Project) proteomics features that has been map to UniProt proteins. You may also refine your search with modifiers such as data_source, peptide etc. See "Arguments section" for more information.

Usage

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

Arguments

accession

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

taxid

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

data_source

Proteomics data source. In addition to manual curation, UniProt also import PTM annotations from the following databases:

Please use `rba_uniprot_proteomics_species()` for more information on the available data sources for a given species.

upid

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

peptide

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

unique

Logical: Should the results be filtered based on the Peptide's uniqueness (the fact that a peptide maps to only 1 protein). If TRUE, Only unique peptides will be returned, if FALSE only un-unique peptides will be returned; If NULL (default) the results will not be filtered based on this.

...

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

Value

A list Where each element correspond to a UniProt protein and proteomics data are organized under the "features" sub-list.

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.

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/ptm"

References

  • The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010, https://doi.org/10.1093/nar/gkae1010

  • Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages 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")
# }