Add missing proteins to PSM-level data based on a fasta database

Usage

adjustProteinAssignments(
  quantification_data,
  fasta_db_path,
  protein_column = "ProteinName",
  peptide_column = "PeptideSequence",
  n_cores = 1,
  keep_unmodified = FALSE
)

Arguments

quantification_data: MS data, preferably in `MSstats` or `MSstatsTMT` format.
fasta_db_path: path to a fasta file that store protein sequences
protein_column: name of a column with protein names.
peptide_column: name of a column with peptide sequences.
n_cores: number of cores that will be used while searching the database.
keep_unmodified: if TRUE, a column that stores sequences of unmodified peptides will be added to output data