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Search Proteomics Peptides in UniProt (Deprecated)

Source: R/deprecated_functions.R
rba_uniprot_proteomics_search.Rd

This function is Deprecated. Please use rba_uniprot_proteomics_non_ptm_search instead.
UniProt maps proteomics peptides from different sources to the proteins' sequences. Using this function, you can search for proteomics peptides 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_search(
  accession = NULL,
  data_source = NULL,
  taxid = 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.

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.

taxid

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

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 Where each element correspond to a UniProt protein and proteomics peptides 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.
see also: Mass spectrometry-based proteomics data in UniProtKB

Corresponding API Resources

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

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 "Deprecated functions": rba_uniprot_proteomics(), rba_uniprot_ptm(), rba_uniprot_ptm_search()

Examples

if (FALSE) { # \dontrun{
#Deprecated
rba_uniprot_proteomics_search(peptide = "MEDYTKIEK")
} # }
if (FALSE) { # \dontrun{
#Deprecated
### this will generate a very large response!
  rba_uniprot_proteomics_search(taxid = 9606,
  data_source = "PeptideAtlas",
  progress = TRUE, timeout = 999999, unique = TRUE)
} # }