QConQuant parameters explained

let qConQuantifierParams = 
    {
    // This will be the name of the peptide data base that is created upon application launch.
    Name                            = "ChlamyTruncDB"
    // This is the directory were the data base will be located. Whenever
    // the application is started the tool looks for data bases in this directory and retrieves their
    // creation parameters. If they are identical to the once in use, the data base will be reused.
    // Note: this also means that this tool will not delete a data base ;) 
    DbFolder                        =  @"C:\Users\david\Source\Repos\netCoreRepos\QConcatifier_Samples\db"
    // This collection of file paths should point to your qConCAT fastas of interest. It is possible to use more than one QconCAT .fasta
    // in one experiment
    QConCatFastaPaths               = [@"C:\Users\david\Source\Repos\netCoreRepos\QConcatifier_Samples\fasta\PS QconCAT.fasta"]
    // The QConCATifier uses the method of target-decoy competition distinct true postive peptide spectrum matches (PSMs) from false positive ones. This data base
    // serves as a codon-unbiased target and decoy source. 
    OrganismFastaPath               =  @"C:\Users\david\Source\Repos\netCoreRepos\QConcatifier_Samples\fasta\Chlamy_JGI5_trunc.fasta"
    // Since .fasta headers are a the wild west of bioinformatics you can specify a regex pattern to parse your protein identifier - if left blank the complete
    // fasta Header will be used in data base creation
    ParseProteinIDRegexPattern      = "id"
    // The protease used for in silico digestion of QConCAT and organism proteins. Note: Should match to the protease used to design the QConCAT. 
    Protease                        = Protease.Trypsin
    // Minimum number of missed cleavages to scan for.
    MinMissedCleavages              = 0
    // Minimum numer of missed cleavages to scan for.
    MaxMissedCleavages              = 1
    // Maximum peptide mass allowed in peptide data base.
    MaxMass                         = 15000.
    // Minimum peptide length allowed in peptide data base.
    MinPepLength                    = 5
    // Maximum peptide length  allowed in peptide data base.
    MaxPepLength                    = 50
    // Isotopic modification used to lable the experiment.
    IsotopicMod                     = [IsotopicMod.N15]
    // Selected mass mode. High accuracy mass spectrometers deliver a resolution that makes it possible to resolve monoisotopic peaks. 
    // If an old instrument is used, the mass mode can be switched to average mass. This is then needed to simulate low resolution theoretical spectra during peptide spectrum
    // matching.
    MassMode                        = MassMode.Monoisotopic
    // If the experimental design led to a permanent modification of a certain amino acid (e.g. carbamidomethylation), this has to be accounted for when computing
    // in silico spectra and retrieving look ups. Here you can specify you modifications.
    FixedMods                       = []            
    // Sometimes the experimental design leads to a variable modification of a certain amino acid (e.g. methionin oxidation) or one is 
    // interested in post translational modification (e.g. phosphorylations). Here you can specify your variable modifications.
    VariableMods                    = []
    // This threshold determines how many variable modifications the user allows to be used for one amino acid. It is not recommended to rise this number to much
    // because it is likely to result in a combinatorial explosion.
    VarModThreshold                 = 3
    // Expected minimum charge, important for calculating theoretically possible mzs of qConCATs
    ExpectedMinCharge               = 2
    // Expected maximum charge, important for calculating theoretically possible mzs of qConCATs
    ExpectedMaxCharge               = 3
    // When a ms2 is recorded, this decision is based on a ion observed in a ms1 scan. The charge and the m/z value of this precursor ion
    // determine the search space. This search window is determined by the theoretical mass +/- x. The x is typically calculated as parts per million
    // of the mass.
    LookUpPPM                       = 30.
    // Determines the scan range when calculating in silico spectra
    ScanRange                       = 100.0,1600.0
    // Determines if the target-decoy competition is used (PepValue) or if the spectra should be filtered solely on the sequest score. 
    PSMThreshold                    = PSMThreshold.PepValue 0.05
    // Determines the scan time window in minutes when extracting a XIC.
    ScanTimeWindow                  = 2.5
    // Determines the m/z window in dalton when extracting a XIC.
    MzWindow_Da                     = 0.07
    // Determines the nterminal series considered when calculating in silico spectra
    NTerminalSeries                 = NTerminalSeries.B
    // Determines the cterminal series considered when calculating in silico spectra
    CTerminalSeries                 = CTerminalSeries.Y
    }