PepMapViz (version 1.1.0)

strip_sequence: Strip peptide sequences based on the specified data type

Description

This function takes outputs from multiple platform, a data frame with a column containing peptide sequences to be stripped, and a column where the stripped sequences will be stored. The function chooses the appropriate stripping method based on the specified data type ('PEAKS', 'Spectronaut', 'MSFragger', 'Comet', 'DIANN', 'Skyline' or 'Maxquant').

Usage

strip_sequence(data, column, convert_column, type)

Value

A data frame with the specified column containing stripped sequences.

Arguments

data

A data frame with the peptide sequences.

column

The name of the column containing the peptide sequences to be stripped.

convert_column

The name of the column where the stripped sequences will be stored.

type

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

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")
)
data_maxquant <- data.table(
  'Modified sequence' = c(
    "_(ac)AAAAELRLLEK_",
    "_EAAENSLVAYK_",
    "_AADTIGYPVM(ox)IRSAYALGGLGSGICPNK_"
  ),
  Condition = c("A", "B", "B")
)

converted_data_skyline <- strip_sequence(data_skyline,
                                         'Peptide Modified Sequence',
                                         'Sequence',
                                         "Skyline")
converted_data_maxquant <- strip_sequence(data_maxquant, 'Modified sequence',
                                          'Sequence', "Maxquant")