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Search Proteomics data in UniProt

Source: R/uniprot_proteomics.R
rba_uniprot_proteomics_non_ptm_search.Rd

Using this function, you can search for non-Post-Translational Modification 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_non_ptm_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/nonPtm"

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_hpp_search(), rba_uniprot_proteomics_non_ptm(), rba_uniprot_proteomics_ptm(), rba_uniprot_proteomics_ptm_search(), rba_uniprot_proteomics_species()

Examples

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