General converter function for MSstatsPTM.

Source: R/globalConverterPTM.R

Requires experimental data, type of spectral processing tool used, and acquisition type. Additionally, the columns containing the protein name and modifications must be indicated

globalConverterPTM(
  data.ptm,
  data.protein = NULL,
  annotation = NULL,
  modification.column,
  processing.tool,
  acquisition.type
)

Arguments

data.ptm

data containing modifications from spectral processing tool
data.protein

data containing unmodified peptides from spectral processing tool
annotation

annotation file if required by MSstats converter. Please view documentation from MSstats or MSstatsTMT for your specific tool.
modification.column

string of column name containing modification information for data.ptm dataset.
processing.tool

name of spectral processing tool for data. Must by one of "SKYLINE", "PROGENESIS", "SPECTRONAUT", "PD", "OPENMS", "OPENSWATH".
acquisition.type

string of "LabelFree" or "TMT". For non-TMT experiments please use "LabelFree"