PepMapViz (version 1.1.0)

obtain_mod: Obtain post translational modification(PTM) information from Peptide data based on the specified data type

Description

This function takes outputs from multiple platform, a data frame with column containing modified peptide sequence with the detailed post translational modification(PTM) information and converts it into a new dataframe with the desired format of peptide sequences and associated PTM information. Due to the flexibility of outputs from multiple platform, the PTM mass to type table needs to be provided if convertion to PTM_type is needed. The result includes 'Peptide', 'PTM_position', 'PTM_type' and 'PTM_mass' columns.The function chooses the appropriate converting method based on the specified data type ('PEAKS', 'Spectronaut', 'MSFragger', 'Comet', 'DIANN', 'Skyline', 'Maxquant', 'mzIdenML' or 'mzTab'), allowing you to convert the data into a consistent format for further analysis.

Usage

obtain_mod(
  data,
  mod_column,
  type,
  seq_column = NULL,
  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 data frame with the peptide sequences.

mod_column

The name of the column containing the modified peptide sequences.

type

A character string specifying the data type (e.g. 'Skyline' or 'Maxquant').

seq_column

(Optional) The name of the column containing peptide sequences for MSFragger, mzid and mzTab. This parameter is required for the "MSFragger", "mzIdenML" and "mzTab" type and can be omitted for other types.

PTM_table

A data frame 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_skyline <- data.table(
  'Peptide Modified Sequence' = c(
    "AGLC[+57]QTFVYGGC[+57]R",
    "AAAASAAEAGIATTGTEDSDDALLK",
    "IVGGWEC[+57]EK"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(
  PTM_mass = c(57.02, -0.98, 15.9949),
  PTM_type = c("Cam", "Amid", "Ox")
)
converted_data_skyline <- obtain_mod(
  data_skyline,
  'Peptide Modified Sequence',
  'Skyline',
  seq_column = NULL,
  PTM_table,
  PTM_annotation = TRUE,
  PTM_mass_column = "PTM_mass"
)

data_maxquant <- data.table(
  'Modified sequence' = c(
    "_(ac)AAAAELRLLEK_",
    "_EAAENSLVAYK_",
    "_AADTIGYPVM(ox)IRSAYALGGLGSGICPNK_"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(
  PTM_mass = c('Phospho (STY)', 'Oxidation (M)'),
  PTM_type = c("Phos", "Ox")
)
converted_data_maxquant <- obtain_mod(
  data_maxquant,
  'Modified sequence',
  'Maxquant',
  seq_column = NULL,
  PTM_table,
  PTM_annotation = TRUE,
  PTM_mass_column = "PTM_mass"
)