Summarise the number of sub-notch PSM intensities per protein

The distribution of TMT intensities obtained by Orbitrap has been observed to have a 'notch' where few values are observed. This function summarises the number of sub-notch values observed per protein

get_notch_per_protein(
  obj,
  master_prot_col = "Master.Protein.Accessions",
  notch_upper = 5.75
)

Arguments

obj

MSnSet containing PSM-level TMT intensities.

master_prot_col

character. Column name for master proteins.

notch_upper

numeric. Upper boundary of notch.

Value

data.frame Summarises # PSMs above/below notch for each protein