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config.py
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config.py
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##### PARAMETERS #####
# name of the mgf file containing the MS2 spectra
SPECTRA_FILE = ["20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf"]
# you can process multiple files like this:
# SPECTRA_FILE = ["20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf", "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_002.mgf"]
# name of the CSM file exported from Proteome Discoverer
CSMS_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.xlsx"
# name of the experiment / run (any descriptive text is allowed)
RUN_NAME = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001-(1)"
# name of the crosslink modification
CROSSLINKER = "DSSO"
# possible modifications and their monoisotopic masses
MODIFICATIONS = \
{"Oxidation": [15.994915],
"Carbamidomethyl": [57.021464],
"DSSO": [54.01056, 85.98264, 103.99320]}
# expected ion types (any of a, b, c, x, y, z)
ION_TYPES = ("b", "y")
# maximum expected charge of fragment ions
MAX_CHARGE = 4
# tolerance for matching peaks
MATCH_TOLERANCE = 0.02
# parameters for calculating iRT
iRT_PARAMS = {"iRT_m": 1.3066, "iRT_t": 29.502}