Table 2.

configurable parameters for pre-processing

name	type	description
remove_carryover	boolean	enables the attempted removal of carryover proteins from a previous run
flter_contaminants	boolean	enables the removal of known contaminants from the prey list
contaminants_file	string	path to file listing all known contaminants in FASTA format
ld_colname	string	column identifier for sample identifier
prey_colname	string	column identifier for identified proteins in data file
pepcount_colname	string	column identifier for observed peptides per protein in data file
mw_colname	string	column identifier for protein molecular weight in data file