# Magnum 1.0.0 alpha 3 parameter file

# This file was autogenerated. Please alter and rename before use.
# All parameters are separated from their values by an equals sign ('=')
# Anything after a '#' will be ignored for the remainder of the line.
# Remove the '#' at the beginning of a parameter line to activate that parameter.


#
# Computational Settings
#
threads = 4
adduct_sites = AEFGHIKLMNPQRSTVWY

#
# Input and Output files - specify full path for input files if not in current working directory
#
MS_data_file = El1_4uLinjection.mzML            #users specify their data here.
database = TestProteome.fasta         #users specify their proteins here.
results_path = .                        #path must exist. Use '.' for current working directory.
export_pepXML = 1                       #0=no, 1=yes
export_percolator = 0                   #0=no, 1=yes
percolator_version = 2.04


#
# Parameters describing data analyzed by Magnum
#
instrument = 0            #0=Orbitrap, 1=FTICR
MS1_centroid = 1          #0=no, 1=yes
MS2_centroid = 1          #0=no, 1=yes
MS1_resolution = 60000    #resolution at 400 m/z, value ignored if data are centroided
MS2_resolution = 15000    #resolution at 400 m/z, value ignored if data are centroided


#
# Amino acid search modification. Use uppercase amino acid letters. n=peptide N-terminus, c=peptide C-terminus
#
fixed_modification = C 57.02146       #fixed modifications are applied to all amino acid instances.
#fixedModification_protN = 15.994915  #fixed modifications to protN are applied to all protein N-termini.
#fixedModification_protc = 15.994915  #fixed modifications to protC are applied to all protein C-termini.
modification = M 15.994915           #modifications are possible (differential) mass alterations.
modification = R 10.008269           #modifications are possible (differential) mass alterations.
modification = K 8.014199           #modifications are possible (differential) mass alterations.
#modification = N 0.984016            #use multiple modification (and fixed_modification) lines for each possible modification mass.
#modification_protN = 42.010565       #modifications to protN are differential on protein N-termini.
#modification_protC = 15.994915       #modifications to protC are differential on protein C-termini.
max_mods_per_peptide = 2              #limit the number of modifications on a peptide (does not include fixed_modifications)
#aa_mass = X 101.074328               #overwrite the default mass on any amino acid. Useful for adding non-canonical amino acids to your search.


#
# Digestion enzyme rules: see http://magnum-ms.org/param/enzyme.html
#
enzyme = [KR]|{P} Trypsin     #must specify rule, followed by enzyme name.
max_miscleavages = 2          #number of missed enzyme cleavages to allow.


#
# Scoring Algorithm Parameters: specifies resolution and fragment ions to search.
#
# fragment_bin_offset and fragment_bin_size influence algorithm precision and memory usage.
# They should be set appropriately for the data analyzed.
# For ion trap ms/ms:  1.0005 size, 0.4 offset
# For high res ms/ms:    0.03 size, 0.0 offset
fragment_bin_size = 0.03      #in m/z units
fragment_bin_offset = 0.0     #between 0.0 and 1.0
ion_series_A = 0              #0=do not search, #1=search
ion_series_B = 1
ion_series_C = 0
ion_series_X = 0
ion_series_Y = 1
ion_series_Z = 0              #Z-dot values are used


#
# Search Space Prameters: specifies breadth of data analysis.
#
decoy_filter = rev_sp      #identifier for all decoys in the database.
e_value_depth = 3000       #robustness of e-value histogram. Larger number improves e-value estimates, but increases computation time.
min_adduct_mass = 5.0     #lowest allowed adduct mass in Daltons.
max_adduct_mass = 600.0    #highest allowed adduct mass in Daltons.

ppm_tolerance_pre = 25.0   #mass tolerance on precursor when searching (in ppm)
precursor_refinement = 1   #0 = off, 1 = attempt to correct precursor prediction errors from MS1 scan.
isotope_error = 3          #search isotope peak offsets. 0=off, 1=one offset, 2=two offsets, 3=three offsets
prefer_precursor_pred = 2  #prefer precursor mono mass predicted by instrument software.
                           #  0 = ignore previous predictions
                           #  1 = use only previous predictions
                           #  2 = supplement predictions with additional analysis

spectrum_processing = 1    #0 = no, 1 = collapse MS2 isotope distributions to a single monoisotopic peak.
min_spectrum_peaks = 20    #minimum peaks in a MS2 scan to be searched.
max_spectrum_peaks = 0     #maximum number of MS2 peaks to use during analysis. 0 uses all peaks.

min_peptide_length = 6     #minimum number of amino acids per peptide searched.
max_peptide_length = 50    #maximum number of amino acids per peptide searched.
min_peptide_mass = 500.0   #minimum allowed peptide mass in Daltons.
max_peptide_mass = 4000.0  #maximum allowed peptide mass in Daltons.


#
# Reporter Ions
#
reporter_ion_threshold = 10.0    #relative MS2 abundance threshold for reporter ions.
#reporter_ion = 160.04           #list as many MS2 reporter ion m/z values as desired, one per line.
#reporter_ion = 311.00
#reporter_ion = 470.03


#
# Diagnostics: Only recommended for advanced users. If enabled, a diagnostic XML file is output with the Magnum results.
#
# diagnostic = 502       #diagnose intermediate peptide calculations for any scan number.
# diagnostic = 503       #list multiple MS2 scan numbers, one per line.
# diagnostic = -1        #or specify -1 to diagnose all MS2 scans.
top_count = 5            #number of lines of candidate peptides to diagnose per precursor prediction per MS2 scan.
truncate_prot_names = 0  #Shorten protein names to just the first number of characters, 0 = off