# ------------------------------------------------------------------
# General Search Parameters
# ------------------------------------------------------------------

ENZYME0=Trypsin (no P rule), Specific, 2 missed cleavages
FIXED_MODIFICATIONS=Carbamidomethylation of C
VARIABLE_MODIFICATIONS=Oxidation of M
REFINEMENT_FIXED_MODIFICATIONS=Carbamidomethylation of C
REFINEMENT_VARIABLE_MODIFICATIONS=
PRECURSOR_MASS_TOLERANCE=10.0
PRECURSOR_MASS_TOLERANCE_UNIT=ppm
FRAGMENT_MASS_TOLERANCE=0.02
FRAGMENT_MASS_TOLERANCE_UNIT=Da
PPM_TO_DA_CONVERSION_REF_MASS=2000.0
FORWARD_FRAGMENT_ION_TYPE=b
FRAGMENT_ION_TYPE_2=y
PRECURSOR_CHARGE_LOWER_BOUND=2
PRECURSOR_CHARGE_UPPER_BOUND=4
ISOTOPIC_CORRECTION_LOWER_BOUND=0
ISOTOPIC_CORRECTION_UPPER_BOUND=1


# ------------------------------------------------------------------
# OMSSA Specific Parameters
# ------------------------------------------------------------------

EVALUE_CUTOFF=100.0
MAXIMUM_HITLIST_LENGTH=10
PRECURSOR_ELIMINATION=false
PRECURSOR_SCALING=true
MINIMAL_PEPTIDE_SIZE=8
MAXIMAL_PEPTIDE_SIZE=30
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS=3
CHARGE_ESTIMATION=true
OUTPUT_TYPE=OMX
MEMORY_MAPPED_SEQUENCES=false
MASS_TO_CONSIDER_EXACT_NEUTRON_MASS=1446.94
LOW_INTENSITY_CUTOFF=0.0
HIGH_INTENSITY_CUTOFF=0.2
INTENSITY_INCREMENT=5.0E-4
SINGLE_CHARGE_WINDOW_WIDTH=27
DOUBLE_CHARGE_WINDOW_WIDTH=14
SINGLE_CHARGE_WINDOW_NPEAKS=2
DOUBLE_CHARGE_WINDOW_NPEAKS=2
MAX_HITS_PER_SPECTRUM_PER_CHARGE=30
MIN_ANNOTATED_INTENSE_PEAKS=6
MIN_ANNOTATED_PEAKS=2
MIN_PEAKS=4
CLEAVE_TERMINAL_METHIONINE=true
MAX_MZ_LADDERS=128
MAX_FRAGMENT_CHARGE=2
FRACTION_PEAKS_FOR_CHARGE_1_ESTIMATION=0.95
AUTO_DETERMINE_CHARGE_ONE=true
SEARCH_POSITIVE_IONS=true
MIN_PERCURSORS_PER_SPECTRUM=1
FORWARD_FRAGMENTS_FIRST=false
REWIND_FRAGMENTS=true
FRAGMENTS_PER_SERIES=100
CORRELATION_CORRECTION_SCORE=true
CONSECUTIVE_ION_PROBABILITY=0.5
ITERATIVE_SEARCH_SEQUENCE_EVALUE=0.0
ITERATIVE_SEARCH_SPECTRUM_EVALUE=0.01
ITERATIVE_SEARCH_REPLACEMENT_EVALUE=0.0


# ------------------------------------------------------------------
# MetaMorpheus Specific Parameters
# ------------------------------------------------------------------

MIN_PEPTIDE_LENGTH=8
MAX_PEPTIDE_LENGTH=30
SEARCH_TYPE=Classic
NUM_PARTITIONS=1
DISSOCIATION_TYPE=HCD
MAX_MODS_FOR_PEPTIDE=2
INITIATOR_METHIONINE_BEHAVIOR=Variable
SCORE_CUTOFF=5.0
USE_DELTA_SCORE=false
FRAGMENTATION_TERMINUS=Both
MAX_FRAGMENTATION_SIZE=30000.0
MASS_DIFF_ACCEPTOR_TYPE=OneMM
WRITE_MZID=true
WRITE_PEPXML=false
USE_PROVIDED_PRECURSOR=true
DO_PREC_DECONVOLUTION=true
DECONVOLUTION_INT_RATIO=3.0
DECONVOLUTION_MASS_TOL=4.0
DECONVOLUTION_MASS_TOL_TYPE=PPM
TRIM_MS1_PEAKS=false
TRIM_MSMS_PEAKS=true
NUM_PEAKS_PER_WINDOWS=200
MIN_ALLOWED_INT_RATIO_TO_BASE_PEAK=0.01
WINDOW_WITH_THOMPSON=null
NUM_WINDOWS=null
NORMALIZE_PEAKS_ACROSS_ALL_WINDOWS=false
MOD_PEPTIDES_ARE_DIFFERENT=false
NO_ONE_HIT_WONDERS=false
SEARCH_TARGET=true
DECOY_TYPE=None
MAX_MOD_ISOFORMS=1024
MIN_VARIANT_DEPTH=1
MAX_HETROZYGOUS_VARIANTS=4
RUN_GPTM=false
GPTMS=Common Biological, Common Artifact, Metal


# ------------------------------------------------------------------
# X!Tandem Specific Parameters
# ------------------------------------------------------------------

DYNAMIC_RANGE=100.0
NUMBER_OF_PEAKS=50
MIN_FRAG_MASS=200.0
MIN_NUMBER_OF_PEAKS=5
NOISE_SUPPRESSION=NO
PARENT_MONOISOTOPIC_MASS_ISOTOPE_ERROR=YES
MIN_PREC_MASS=500.0
PROTEIN_QUICK_ACETYL=YES
QUICK_PYROLIDONE=YES
PROTEIN_PTM_COMPLEXITY=6.0
STP_BIAS=NO
REFINE=YES
REFINE_SEMI=NO
REFINE_POINT_MUTATIONS=NO
REFINE_SPECTRUM_SYNTHESIS=YES
REFINE_UNANTICIPATED_CLEABAGES=YES
REFINE_SNAPS=YES
REFINE_MAX_EVALUE=0.01
POTENTIAL_MODIFICATIONS_FOR_FULL_REFINEMENT=NO
EVALUE_CUTOFF=0.01
SKYLINE_PATH=
OUTPUT_RESULTS=all
OUTPUT_PROTEINS=YES
OUTPUT_SEQUENCES=NO
OUTPUT_SPECTRA=YES
OUTPUT_HISTOGRAMS=NO


# ------------------------------------------------------------------
# PepNovo+ Specific Parameters
# ------------------------------------------------------------------

HIT_LIST_LENGTH=10
CORRECT_PRECURSOR_MASS=false
DISCARD_LOW_QUALITY_SPECTRA=true
FRAGMENTATION_MODEL=CID_IT_TRYP
GENERATE_QUERY=false


# ------------------------------------------------------------------
# Andromeda Specific Parameters
# ------------------------------------------------------------------

MIN_PEPTIDE_LENGHT_NO_ENZYME=8
MAX_PEPTIDE_LENGHT_NO_ENZYME=30
MAX_PEPTIDE_MASS=4600.0
NUMBER_SPECTRUM_MATCHES=10
MAX_PTMS=5
FRAGMENTATION_METHOD=CID
WATER_LOSS=true
AMMONIA_LOSS=true
SEQUENCE_DEPENDENT_NEUTRAL_LOSS=true
EQUAL_IL=false
FRAGMENT_ALL=false
EMPERICAL_CORRECTION=true
HIGHER_CHARGE=true
MAX_COMBINATIONS=250
TOP_PEAKS=8
TOP_PEAKS_WINDOW=100
DECOY_MODE=none


# ------------------------------------------------------------------
# MS Amanda Specific Parameters
# ------------------------------------------------------------------

SEARCH_DECOY=false
REPORT_BOTH_BEST_HITS_FOR_TD=true
INSTRUMENT_ID=b, y
MONOISOTOPIC=true
MAX_RANK=10
PERFORM_DEISOTOPING=true
MAX_MODIFICATIONS=3
MAX_VARIABLE_MODIFICATIONS=4
MAX_MODIFICATIONS_SITES=6
MAX_NEUTRAL_LOSSES=1
MAX_NEUTRAL_LOSSES_PER_MODIFICATION=2
MIN_PEPTIDE_LENGTH=8
MAX_PEPTIDE_LENGTH=30
MAX_LOADED_PROTEINS=100000
MAX_LOADED_SPECTRA=2000
OUTPUT_FORMAT=csv


# ------------------------------------------------------------------
# MS-GF+ Specific Parameters
# ------------------------------------------------------------------

SEARCH_DECOY=false
INSTRUMENT_ID=3
FRAGMENTATION_ID=3
PROTOCOL_ID=0
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
NUMBER_SPECTRUM_MATCHES=10
ADDITIONAL_OUTPUT=false
NUMBER_OF_TOLERABLE_TERMINI=2
MAX_NUMBER_MODIFICATIONS=2
NUMBER_TASKS=null


# ------------------------------------------------------------------
# DirecTag Specific Parameters
# ------------------------------------------------------------------

TIC_CUTOFF_PERCENTAGE=100.0
MAX_PEAK_COUNT=100
NUM_INTENSITY_CLASSES=3
ADJUST_PRECURSOR_MASS=false
MIN_PRECUSOR_ADJUSTMENT=-0.5
MAX_PRECUSOR_ADJUSTMENT=1.5
PRECUSOR_ADJUSTMENT_STEP=0.1
NUM_CHARGE_STATES=3
OUTPUT_SUFFIX=
USE_CHARGE_STATE_FROM_MS=true
DUPLICATE_SPECTRA=true
DEISOTOPING_MODE=0
ISOTOPE_MZ_TOLERANCE=0.25
COMPLEMENT_MZ_TOLERANCE=0.1
TAG_LENGTH=4
MAX_DYNAMIC_MODS=2
MAX_TAG_COUNT=10
INTENSITY_SCORE_WEIGHT=1.0
MZ_FIDELITY_SCORE_WEIGHT=1.0
COMPLEMENT_SCORE_WEIGHT=1.0


# ------------------------------------------------------------------
# Comet Specific Parameters
# ------------------------------------------------------------------

NUMBER_SPECTRUM_MATCHES=10
MAX_VARIABLE_MODS=10
REQUIRE_VARIABLE_MODS=false
MIN_PEAKS=10
MIN_PEAKS_INTENSITY=0.0
REMOVE_PRECURSOR=0
REMOVE_PRECURSOR_TOLERANCE=1.5
LOWER_CLEAR_MZ_RANGE=0.0
UPPER_CLEAR_MZ_RANGE=0.0
ENZYME_TYPE=2
ISOTOPE_CORRECTION=1
MIN_PRECURSOR_MASS=600.0
MAX_PRECURSOR_MASS=5000.0
MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
MAX_FRAGMENT_CHARGE=3
REMOVE_METHIONINE=false
BATCH_SIZE=0
THEORETICAL_FRAGMENT_IONS_SUM_ONLY=false
FRAGMENT_BIN_OFFSET=0.01

USE_SPARSE_MATRIX=true
OUTPUT_FORAMT=PepXML
PRINT_EXPECT_SCORE=true


# ------------------------------------------------------------------
# MyriMatch Specific Parameters
# ------------------------------------------------------------------

MIN_PEP_LENGTH=8
MAX_PEP_LENGTH=30
NUMBER_SPECTRUM_MATCHES=10
TIC_CUTOFF_PERCENTAGE=0.98
MAX_DYNMIC_MODS=2
MIN_TERMINI_CLEAVAGES=2
MIN_PRECURSOR_MASS=600.0
MAX_PRECURSOR_MASS=5000.0
USE_SMART_PLUS_THREE_MODEL=false
COMPUTE_XCORR=false
NUM_INTENSITY_CLASSES=3
CLASS_SIZE_MULTIPLIER=2
NUM_BATCHES=50
FRAGMENTATION_RULE=CID
MAX_PEAK_COUNT=300
OUTPUT_FORMAT=mzIdentML


# ------------------------------------------------------------------
# pNovo+ Specific Parameters
# ------------------------------------------------------------------

NUMBER_PEPTIDES=10
LOWER_PRECURSOR_MASS=300
UPPER_PRECURSOR_MASS=5000
ACTIVATION_TYPE=HCD


# ------------------------------------------------------------------
# Tide Specific Parameters
# ------------------------------------------------------------------

MIN_PEP_LENGTH=6
MAX_PEP_LENGTH=30
MIN_PRECURSOR_MASS=200.0
MAX_PRECURSOR_MASS=7200.0
MAX_VARIABLE_MODIFICATIONS_PER_TYPE_PER_PEPTIDE=2
MAX_VARIABLE_MODIFICATIONS_PER_PEPTID=255
DECOY_FORMAT=none
KEEP_TERMINAL_AMINO_ACIDS=NC
DECOY_SEED=1
OUTPUT_FOLDER_NAME=crux-output
PRINT_PEPTIDES=false
VERBOSITY=30
MONOISOTOPIC_PRECURSOR=true
CLIP_NTERM_METHIONINE=false
DIGESTION_TYPE=full-digest
COMPUTE_SP_SCORE=false
NUMBER_SPECTRUM_MATCHES=10
COMPUTE_EXACT_P_VALUES=false
MIN_SPECTRUM_MZ=0.0
MAX_SPECTRUM_MZ=null
MIN_SPECTRUM_PEAKS=20
SPECTRUM_CHARGES=all
REMOVE_PRECURSOR=false
REMOVE_PRECURSOR_TOLERANCE=1.5
PRINT_PROGRESS_INDICATOR_SIZE=1000
USE_FLANKING_PEAKS=false
USE_NEUTRAL_LOSS_PEAKS=false
MZ_BIN_WIDTH=0.02
MZ_BIN_OFFSET=0.0
CONCATENATE_TARGET_DECOY=false
STORE_SPECTRA_FILE_NAME=null
TEXT_OUTPUT=true
SQT_OUTPUT=false
PEPXML_OUTPUT=false
MZID_OUTPUT=false
PERCOLATOR_OUTPUT=false


# ------------------------------------------------------------------
# Novor Specific Parameters
# ------------------------------------------------------------------

FRAGMENTATION=HCD
MASS_ANALYZER=FT