## The parameter 'name' defines the name of this lipid class.
name=O-PC
## When set to 'true', the parameter 'adductInsensitiveRtFilter' forces the RT filter to be calculated based on all modifications
adductInsensitiveRtFilter=false
## When set to 'true', the parameter 'pickBestMatchBySpectrumCoverage' the best matches are picked from duplicates (same lipid class and scan number) by spectrum coverage.
pickBestMatchBySpectrumCoverage=false
## Number of OH groups present in the fatty acyl (FA) and long chain base (LCB) chains of this lipid class, 
## where the parameter 'OH_number' defines which number the values should be explicitly written in the mass list for 
## and 'OH_range_from' and 'OH_range_to' define the lower and upper limit of the number of OH groups, respectively, which the algorithm identifies compounds for. 
## Which number is chosen for 'OH_number' from the biologically relevant range does not influence the algorithm. 
## ATTENTION: this parameter should only be used for sphingolipids. 
OH_number=0
OH_range_from=0
OH_range_to=0
## Optional definition of the retention time (RT) range (the lower limit is defined with 'RT_range_from' and the upper limit with 'RT_range_to') that this lipid class elutes at. 
RT_range_from=-1.0
RT_range_to=-1.0
## Number of oxidation sites on the FA chains of this lipid class, with 'Ox_range_from' and 'Ox_range_to' referring to the lower and upper limits. 
## ATTENTION: this parameter should be used for oxidized lipid classes other than sphingolipids 
Ox_range_from=0
Ox_range_to=0
## The parameter 'adducts' allows for the definition of adducts relevant for this lipid class. 
## The given names must correspond to names (parameter 'name') of adducts defined in .txt files in the folder ./massListCreation/adducts 
## Multiple names are separated with a comma and no spaces, e.g. adductName1,adductName2,adductName3 
adducts=HCOO
## The parameter 'headgroup_formula' defines the chemical formula of the headgroup (without chains) 
headgroup_formula=C8H18O7P1N1
## The parameters 'min_chain_C' and 'max_chain_C' describe the minimum and maximum total number of C atoms in chains to be included in the mass list 
min_chain_C=20
max_chain_C=48
## The parameters 'min_chain_DB' and 'max_chain_DB' describe the minimum and maximum total number of double bonds in chains to be considered in the mass list 
min_chain_DB=0
max_chain_DB=12
## The parameter 'number_of_FA_chains' allows for the definition of the number of FA and/or LCB chains present in this lipid class.
number_of_FA_chains=2
## The parameter 'number_of_SPB_chains' allows for the definition of the number of LCB chains present in this lipid class. 
number_of_SPB_chains=0
## The parameter 'FA_chain_list_name' allows for the definition of a FA chain list name (without suffix, must be present in the folder ./fattyAcids) to base the mass list on. 
## Only compounds that are possible given the entries in the provided chain list will be included in the resulting mass list. 
## If the chain list includes stable isotope labeled chains, those will be included in all possible combinations in the generated mass list file. 
FA_chain_list_name=fattyAcidChains
## The parameter 'SPB_chain_list_name' allows for the definition of a LCB chain list name (without suffix, must be present in the folder ./fattyAcids) to base the mass list on. 
## Only compounds that are possible given the entries in the provided chain list will be included in the resulting mass list. 
## If the chain list includes stable isotope labeled chains, those will be included in all possible combinations in the generated mass list file. 
SPB_chain_list_name=
