config.toml

[ms2pip]
model = "HCD"
frag_error = "0.02"
out = "csv"
ptm = [
    "PhosphoS,79.966331,opt,S",
    "PhosphoT,79.966331,opt,T",
    "PhosphoY,79.966331,opt,Y",
    "Oxidation,15.994915,opt,M",
    "Carbamidomethyl,57.021464,opt,C",
    "CAM,57.021464,opt,C",
    "Glu->pyro-Glu,-18.010565,opt,E",
    "Gln->pyro-Glu,-17.026549,opt,Q",
    "Pyro-cmC,39.994915,opt,C",
    "Deamidated,0.984016,opt,N",
    "iTRAQ,144.102063,opt,N-term",
    "Acetyl,42.010565,opt,N-term",
    "TMT6plexN,229.162932,opt,N-term",
    "TMT6plex,229.162932,opt,K"
]
sptm = []
gptm = []

# Only applicable if --retention-time option is used
# deeplc settings are passed to DeepLC() object as keyword arguments
[deeplc]
calibration_file = false
verbose = false
path_model = false # Path to DeepLC model
split_cal = 25 # Can maximally be number of calibration peptides - 1
batch_num = 350000 # Reduce to limit memory consumption