PepMapViz (version 1.1.0)

obtain_mod_Spectronaut: Obtain modification information from Peptide data generated by Spectronaut

Description

This function takes Spectronaut 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_Spectronaut(
  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 modified peptide sequences.

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(
  EG.ModifiedPeptide = c(
    "_[Acetyl (Protein N-term)]M[Oxidation (M)]DDREDLVYQAK_",
    "_EAAENSLVAYK_",
    "_IEAELQDIC[Carbamidomethyl (C)]NDVLELLDK_"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(
  PTM_mass = c(
    'Acetyl (Protein N-term)',
    'Oxidation (M)',
    'Carbamidomethyl (C)'
  ),
  PTM_type = c("Acet", "Ox", "Cam")
)
converted_data <- obtain_mod_Spectronaut(data, 'EG.ModifiedPeptide',
                                         PTM_table, PTM_annotation = TRUE,
                                         PTM_mass_column = "PTM_mass")
data <- data.table(
  EG.IntPIMID = c(
    "_[+42]M[-0.98]DDREDLVYQAK_",
    "_EAAENSLVAYK_",
    "_IEAELQDIC[+57]NDVLELLDK_"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(PTM_mass = c(42, -0.98, 57),
                        PTM_type = c("Acet", "Amid", "Cam"))
PTM_mass_column <- "PTM_mass"
converted_data <- obtain_mod_Spectronaut(data,
                                         'EG.IntPIMID',
                                         PTM_table,
                                         PTM_annotation = TRUE,
                                         PTM_mass_column)