config.toml

# Configuration file

# For overlaid figures, Half Window size of the view (+- center):
MZVIEWHALFWINDOW = 0.7
RTVIEWHALFWINDOW = 1.5
ATVIEWHALFWINDOW = 2

# Mass tolerance for chromatogram extraction, Half Window m/z value (+- center or m/z target):
MZXICHALFWINDOW = 0.01

# Error thresholds, absolute value:
MZERRORPPM = 15
RTERROR = 0.3
ATERROR = 0.1
ABUNDANCEERROR = 30 # Percentage absolute error, a percentage of the mean of the ion abundance applied as a threshold to report QC ions outside tolerances

AutoTrackedIonsTopN = 4 # Number of auto-tracked ions to detect per sample group
MinIntensityPresencePercentage = 80 # Intensity threshold presence/absence 

MinMzDistDetectCentroidMS = 0.0005 # If distance between 2 consecutive points from the max intensity peak is smaller than this value then it is considered profile mode spectrum

FigureLegendMaxNumberLines = 15

# MZA conversion:
MinIntensityMza = 20

# time-vs-mz images:
TimeVsMzImageMinIntensityPercentage = 10
TimeVsMzImageMaxIntensityCeilingPercentage = 70