annotate_peptides: Annotate peptides based on their enzyme specificity and...

In MiguelCos/fragNterminomics: Annotation and processing of peptides from FragPipe search results

Annotate peptides based on their enzyme specificity and position within protein sequence.

Description

Annotate peptides based on their enzyme specificity and position within protein sequence.

Usage

annotate_peptides(
  peptide2protein,
  fasta,
  decoy_tag = "^rev",
  specificity = "R|K"
)

Arguments

peptide2protein	A data frame with at least two columns: 'Peptide' (peptide sequence to annotate) and 'Genes' (Uniprot ID of associated protein).
fasta	A list of identified protein sequences, at least matching the ones present in the 'peptide2protein' data frame. This list should should be loaded into R with the 'read.fasta' function from the 'seqinr' package. You need to set the argument as.string=TRUE.
decoy_tag	A string with the tag of the decoy sequences.
specificity	A string defining the enzyme specificity.

Value

a data frame with annotation information of the input peptides.

MiguelCos/fragNterminomics documentation built on Oct. 13, 2023, 5:31 a.m.