PepMapViz (version 1.1.0)

obtain_mod_PEAKS: Obtain modification information from Peptide data generated by PEAKS

Description

This function takes PEAKS 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_PEAKS(
  data,
  mod_column,
  PTM_table = NULL,
  PTM_annotation = FALSE,
  PTM_mass_column
)

Value

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

Arguments

data

A dataframe with a column containing modified peptide sequences.

mod_column

The name of the column containing the modified peptide sequences.

PTM_table

A dataframe 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(
  Peptide = c(
    "AAN(+42)Q(-0.98)RGSLYQCDYSTGSC(+57.02)EPIR",
    "K.AAQQTGKLVHANFGT.K",
    "K.(-0.98)AATVTGKLVHANFGT.K"
  ),
  Sequence = c(
    "AANQRGSLYQCDYSTGSCEPIR",
    "AAQQTGKLVHANFGT",
    "AATVTGKLVHANFGT"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(PTM_mass = c(42, -0.98, 57.02),
                        PTM_type = c("Acet", "Amid", "Cam"))
mod_column <- "Peptide"
PTM_mass_column <- "PTM_mass"
converted_data <- obtain_mod_PEAKS(data, mod_column, PTM_table,
PTM_annotation = TRUE, PTM_mass_column)