PepMapViz (version 1.1.0)

obtain_mod_DIANN: Obtain modification information from Peptide data generated by DIA-NN

Description

This function takes DIA-NN 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_DIANN(
  data,
  mod_column,
  PTM_table = NULL,
  PTM_annotation = FALSE,
  PTM_mass_column
)

Value

A dataframe with 'Peptide', 'PTM_position', and 'PTM_type' columns.

Arguments

data

A dataframe with 'Stripped.Sequence' column and 'Modified.Sequence' 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(
  Modified.Sequence = c(
    "AAAAGPGAALS(UniMod:21)PRPC(UniMod:4)DSDPATPGAQSPK",
    "AAAASAAEAGIATTGTEDSDDALLK",
    "AAAAALSGSPPQTEKPT(UniMod:21)HYR"
  ),
  Stripped.Sequence = c(
    "AAAAGPGAALSPRPCDSDPATPGAQSPK",
    "AAAASAAEAGIATTGTEDSDDALLK",
    "AAAAALSGSPPQTEKPTHYR"
  ),
  Condition = c("A", "B", "B")
)
PTM_table <- data.table(PTM_mass = c('UniMod:21', 'UniMod:4'),
                        PTM_type = c("Phos", "Cam"))
converted_data <- obtain_mod_DIANN(
  data,
  'Modified.Sequence',
  PTM_table,
  PTM_annotation = TRUE,
  PTM_mass_column = "PTM_mass"
)