PepMapViz (version 1.1.0)

obtain_mod_Comet: Obtain modification information from Peptide data generated by Comet

Description

This function takes Comet output containing a column with modified peptide sequences including PTM information and converts it into a new dataframe with the desired format of peptide sequences and associated PTM information.

Usage

obtain_mod_Comet(
  data,
  mod_column,
  PTM_table = NULL,
  PTM_annotation = FALSE,
  PTM_mass_column
)

Value

A data.table with 'PTM_position', 'PTM_type', 'reps', and other columns.

Arguments

data

A data.table with a column containing PTM information.

mod_column

The name of the column containing the modified peptide sequences.

PTM_table

A data.table with columns 'PTM_mass' and 'PTM_type' containing PTM annotation information.

PTM_annotation

A logical value indicating whether to include PTM annotation information in the result.

PTM_mass_column

The name of the column containing the PTM mass information

Examples

library(data.table)
data <- data.table(
  modified_peptide = c(
    "AAM[15.9949]Q[-0.98]RGSLYQCDYSTGSC[57.02]EPIR",
    "K.AAQQTGKLVHANFGT.K",
    "K.[-0.98]AATVTGKLVHANFGT.K"
  ),
  plain_peptide = c(
    "AAMQRGSLYQCDYSTGSCEPIR",
    "AAQQTGKLVHANFGT",
    "AATVTGKLVHANFGT"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(
  PTM_mass = c(57.02, -0.98, 15.9949),
  PTM_type = c("Cam", "Amid", "Ox")
)
mod_column <- 'modified_peptide'
PTM_mass_column <- "PTM_mass"
converted_data <- obtain_mod_Comet(data, mod_column, PTM_table,
PTM_annotation = TRUE, PTM_mass_column)