Crux parameters

 assign-confidencecascade-searchcometcomet-indexcreate-docsbullseyehardklorlfqgenerate-peptidesget-ms2-spectrumkojakmake-pinlocalize-modificationparam-medicpercolatorpipelinepredict-peptide-ionsprint-processed-spectrapsm-convertread-tide-indexspectral-countssubtract-indextide-indextide-searchdiameterspectrum-converter
estimation-method✓✓             ✓          
decoy-prefix✓✓      ✓  ✓  ✓✓      ✓   
score✓✓             ✓          
sidak✓✓             ✓          
top-match-in✓✓             ✓          
verbosity✓✓✓✓ ✓✓✓✓✓✓✓✓✓✓✓ ✓✓ ✓✓✓✓✓✓
parameter-file✓✓✓✓ ✓✓✓✓ ✓✓✓✓✓✓ ✓✓ ✓✓✓✓ ✓
overwrite✓✓✓✓ ✓✓✓✓ ✓✓✓✓✓✓ ✓✓ ✓✓✓✓✓✓
output-dir✓✓✓✓ ✓✓✓✓ ✓✓✓✓✓✓  ✓ ✓✓✓✓✓✓
list-of-files✓✓             ✓          
combine-charge-states✓✓             ✓          
combine-modified-peptides✓✓             ✓          
fileroot✓✓✓✓ ✓✓✓✓ ✓✓ ✓✓✓    ✓  ✓ ✓
q-value-threshold ✓                        
auto-mz-bin-width ✓             ✓       ✓  
auto-precursor-window ✓             ✓       ✓  
concat ✓             ✓       ✓  
deisotope ✓             ✓       ✓  
fragment-tolerance ✓             ✓       ✓  
isotope-error ✓             ✓       ✓  
mass-precision ✓             ✓     ✓✓✓  
max-precursor-charge ✓             ✓       ✓✓ 
min-precursor-charge ✓             ✓       ✓  
min-peaks ✓             ✓       ✓  
mod-precision ✓      ✓   ✓  ✓      ✓✓  
mz-bin-offset ✓             ✓       ✓✓ 
mz-bin-width ✓             ✓       ✓✓ 
mzid-output ✓            ✓✓       ✓  
mztab-output ✓             ✓       ✓  
num-threads ✓     ✓       ✓       ✓ ✓
override-charges ✓             ✓       ✓  
pepxml-output ✓             ✓       ✓  
pin-output ✓             ✓       ✓  
pm-charges ✓✓✓      ✓  ✓ ✓       ✓  
pm-max-frag-mz ✓✓✓      ✓  ✓ ✓       ✓  
pm-max-precursor-delta-ppm ✓✓✓      ✓  ✓ ✓       ✓  
pm-max-precursor-mz ✓✓✓      ✓  ✓ ✓       ✓  
pm-max-scan-separation ✓✓✓      ✓  ✓ ✓       ✓  
pm-min-common-frag-peaks ✓✓✓      ✓  ✓ ✓       ✓  
pm-min-frag-mz ✓✓✓      ✓  ✓ ✓       ✓  
pm-min-peak-pairs ✓✓✓      ✓  ✓ ✓       ✓  
pm-min-precursor-mz ✓✓✓      ✓  ✓ ✓       ✓  
pm-min-scan-frag-peaks ✓✓✓      ✓  ✓ ✓       ✓  
pm-pair-top-n-frag-peaks ✓✓✓      ✓  ✓ ✓       ✓  
pm-top-n-frag-peaks ✓✓✓      ✓  ✓ ✓       ✓  
precision ✓             ✓       ✓  
precursor-window ✓             ✓       ✓  
precursor-window-type ✓             ✓       ✓  
print-search-progress ✓             ✓       ✓  
remove-precursor-peak ✓             ✓       ✓  
remove-precursor-tolerance ✓       ✓     ✓       ✓  
scan-number ✓       ✓     ✓       ✓  
score-function ✓             ✓       ✓  
skip-preprocessing ✓             ✓       ✓  
spectrum-max-mz ✓             ✓       ✓  
spectrum-min-mz ✓             ✓       ✓  
spectrum-parser ✓     ✓ ✓   ✓ ✓ ✓  ✓  ✓  
sqt-output ✓             ✓       ✓  
store-index ✓             ✓       ✓  
store-spectra ✓             ✓       ✓  
txt-output ✓            ✓✓       ✓  
use-flanking-peaks ✓             ✓       ✓  
use-neutral-loss-peaks ✓             ✓       ✓  
use-z-line ✓       ✓     ✓ ✓     ✓  
decoy_search  ✓✓           ✓          
peff_format  ✓✓           ✓          
peff_obo  ✓✓           ✓          
num_threads  ✓✓           ✓          
peptide_mass_tolerance  ✓✓           ✓          
peptide_mass_tolerance_lower  ✓✓           ✓          
peptide_mass_tolerance_upper  ✓✓           ✓          
auto_peptide_mass_tolerance  ✓✓           ✓          
peptide_mass_units  ✓✓           ✓          
mass_type_parent  ✓✓           ✓          
mass_type_fragment  ✓✓           ✓          
precursor_tolerance_type  ✓✓           ✓          
isotope_error  ✓✓           ✓          
search_enzyme_number  ✓✓           ✓          
search_enzyme2_number  ✓✓           ✓          
num_enzyme_termini  ✓✓           ✓          
allowed_missed_cleavage  ✓✓           ✓          
fragment_bin_tol  ✓✓           ✓          
fragment_bin_offset  ✓✓      ✓    ✓          
auto_fragment_bin_tol  ✓✓           ✓          
theoretical_fragment_ions  ✓✓           ✓          
use_A_ions  ✓✓           ✓          
use_B_ions  ✓✓           ✓          
use_C_ions  ✓✓           ✓          
use_X_ions  ✓✓           ✓          
use_Y_ions  ✓✓           ✓          
use_Z_ions  ✓✓           ✓          
use_Z1_ions  ✓✓           ✓          
use_NL_ions  ✓✓           ✓          
output_mzidentmlfile  ✓✓           ✓          
output_pepxmlfile  ✓✓           ✓          
output_percolatorfile  ✓✓           ✓          
output_sqtfile  ✓✓           ✓          
output_sqtstream  ✓✓           ✓          
output_txtfile  ✓✓           ✓          
num_output_lines  ✓✓           ✓          
scan_range  ✓✓           ✓          
precursor_charge  ✓✓           ✓          
override_charge  ✓✓           ✓          
ms_level  ✓✓           ✓          
activation_method  ✓✓           ✓          
clip_nterm_methionine  ✓✓           ✓          
decoy_prefix  ✓✓           ✓          
digest_mass_range  ✓✓           ✓          
equal_I_and_L  ✓✓           ✓          
mass_offsets  ✓✓           ✓          
max_duplicate_proteins  ✓✓           ✓          
max_fragment_charge  ✓✓           ✓          
max_precursor_charge  ✓✓           ✓          
num_results  ✓✓           ✓          
nucleotide_reading_frame  ✓✓           ✓          
output_suffix  ✓✓           ✓          
peptide_length_range  ✓✓           ✓          
precursor_NL_ions  ✓✓           ✓          
spectrum_batch_size  ✓✓           ✓          
text_file_extension  ✓✓           ✓          
resolve_fullpaths  ✓✓           ✓          
pinfile_protein_delimiter  ✓✓           ✓          
minimum_peaks  ✓✓           ✓          
minimum_intensity  ✓✓           ✓          
remove_precursor_peak  ✓✓           ✓          
remove_precursor_tolerance  ✓✓           ✓          
clear_mz_range  ✓✓           ✓          
variable_mod01  ✓✓           ✓          
variable_mod02  ✓✓           ✓          
variable_mod03  ✓✓           ✓          
variable_mod04  ✓✓           ✓          
variable_mod05  ✓✓           ✓          
variable_mod06  ✓✓           ✓          
variable_mod07  ✓✓           ✓          
variable_mod08  ✓✓           ✓          
variable_mod09  ✓✓           ✓          
variable_mod10  ✓✓           ✓          
variable_mod11  ✓✓           ✓          
variable_mod12  ✓✓           ✓          
variable_mod13  ✓✓           ✓          
variable_mod14  ✓✓           ✓          
variable_mod15  ✓✓           ✓          
auto_modifications  ✓✓           ✓          
max_variable_mods_in_peptide  ✓✓           ✓          
require_variable_mod  ✓✓           ✓          
protein_modlist_file  ✓✓           ✓          
add_Cterm_peptide  ✓✓           ✓          
add_Nterm_peptide  ✓✓           ✓          
add_Cterm_protein  ✓✓           ✓          
add_Nterm_protein  ✓✓           ✓          
add_A_alanine  ✓✓           ✓          
add_C_cysteine  ✓✓           ✓          
add_D_aspartic_acid  ✓✓           ✓          
add_E_glutamic_acid  ✓✓           ✓          
add_F_phenylalanine  ✓✓           ✓          
add_G_glycine  ✓✓           ✓          
add_H_histidine  ✓✓           ✓          
add_I_isoleucine  ✓✓           ✓          
add_K_lysine  ✓✓           ✓          
add_L_leucine  ✓✓           ✓          
add_M_methionine  ✓✓           ✓          
add_N_asparagine  ✓✓           ✓          
add_O_pyrrolysine  ✓✓           ✓          
add_P_proline  ✓✓           ✓          
add_Q_glutamine  ✓✓           ✓          
add_R_arginine  ✓✓           ✓          
add_S_serine  ✓✓           ✓          
add_T_threonine  ✓✓           ✓          
add_U_selenocysteine  ✓✓           ✓          
add_V_valine  ✓✓           ✓          
add_W_tryptophan  ✓✓           ✓          
add_Y_tyrosine  ✓✓           ✓          
add_B_user_amino_acid  ✓✓           ✓          
add_J_user_amino_acid  ✓✓           ✓          
add_X_user_amino_acid  ✓✓           ✓          
add_Z_user_amino_acid  ✓✓           ✓          
fragindex_skipreadprecursors  ✓✓           ✓          
fragindex_num_spectrumpeaks  ✓✓           ✓          
fragindex_min_ions_score  ✓✓           ✓          
fragindex_min_ions_report  ✓✓           ✓          
fragindex_min_fragmentmass  ✓✓           ✓          
fragindex_max_fragmentmass  ✓✓           ✓          
create_peptide_index   ✓                      
max-persist     ✓         ✓          
exact-match     ✓         ✓          
exact-tolerance     ✓         ✓          
persist-tolerance     ✓         ✓          
gap-tolerance     ✓         ✓          
scan-tolerance     ✓         ✓          
bullseye-max-mass     ✓         ✓          
bullseye-min-mass     ✓         ✓          
retention-tolerance     ✓         ✓          
spectrum-format     ✓         ✓          
hardklor-algorithm      ✓                   
averagine-mod      ✓                   
boxcar-averaging      ✓                   
boxcar-filter      ✓                   
boxcar-filter-ppm      ✓                   
centroided      ✓                   
cdm      ✓                   
min-charge      ✓                   
max-charge      ✓                   
corr      ✓                   
depth      ✓                   
distribution-area      ✓                   
hardklor-data-file      ✓                   
instrument      ✓                   
isotope-data-file      ✓                   
max-features      ✓                   
mzxml-filter      ✓                   
mz-max      ✓                   
mz-min      ✓                   
mz-window      ✓                   
resolution      ✓                   
scan-range-max      ✓                   
scan-range-min      ✓                   
sensitivity      ✓                   
signal-to-noise      ✓                   
smooth      ✓                   
sn-window      ✓                   
static-sn      ✓                   
num-isotopes-required       ✓                  
peak-finding-ppm-tolerance       ✓                  
ppm-tolerance       ✓                  
id-specific-charge-state       ✓                  
missed-scans-allowed       ✓                  
isotope-tolerance-ppm       ✓                  
integrate       ✓                  
discrimination-factor-to-cut-peak       ✓                  
quantify-ambiguous-peptides       ✓                  
use-shared-peptides-for-protein-quant       ✓                  
normalize       ✓                  
specfile-replicates       ✓                  
psm-file-format       ✓                  
is-rt-seconds       ✓                  
mods-spec       ✓       ✓      ✓   
nterm-peptide-mods-spec       ✓       ✓      ✓   
cterm-peptide-mods-spec       ✓       ✓      ✓   
lfq-q-value-threshold       ✓                  
is-psm-filtered       ✓                  
min-mass        ✓      ✓      ✓   
max-mass        ✓      ✓      ✓   
min-length        ✓      ✓      ✓   
max-length        ✓      ✓      ✓   
enzyme        ✓      ✓      ✓   
custom-enzyme        ✓      ✓      ✓   
digestion        ✓      ✓      ✓   
missed-cleavages        ✓      ✓      ✓   
isotopic-mass        ✓      ✓      ✓   
seed        ✓      ✓      ✓   
clip-nterm-methionine        ✓      ✓      ✓   
decoy-format        ✓      ✓      ✓   
keep-terminal-aminos        ✓      ✓      ✓   
stats         ✓                
threads          ✓               
export_percolator          ✓               
export_mzID          ✓               
export_pepXML          ✓               
enrichment          ✓               
MS1_centroid          ✓               
MS2_centroid          ✓               
MS1_resolution          ✓               
MS2_resolution          ✓               
cross_link          ✓               
mono_link          ✓               
fixed_modification          ✓               
fixed_modification_protC          ✓               
fixed_modification_protN          ✓               
modification          ✓               
modification_protC          ✓               
modification_protN          ✓               
diff_mods_on_xl          ✓               
max_mods_per_peptide          ✓               
mono_links_on_xl          ✓               
fragment_bin_size          ✓               
auto_fragment_bin_size          ✓               
ion_series_A          ✓               
ion_series_B          ✓               
ion_series_C          ✓               
ion_series_X          ✓               
ion_series_Y          ✓               
ion_series_Z          ✓               
decoy_filter          ✓               
max_miscleavages          ✓               
max_peptide_mass          ✓               
min_peptide_mass          ✓               
min_peptide_score          ✓               
min_spectrum_peaks          ✓               
max_spectrum_peaks          ✓               
ppm_tolerance_pre          ✓               
auto_ppm_tolerance_pre          ✓               
precursor_refinement          ✓               
prefer_precursor_pred          ✓               
spectrum_processing          ✓               
top_count          ✓               
e_value_depth          ✓               
truncate_prot_names          ✓               
kojak_instrument          ✓               
kojak_enzyme          ✓               
kojak_isotope_error          ✓               
max-charge-feature           ✓  ✓✓          
output-file           ✓              
top-match           ✓✓ ✓✓       ✓✓ 
unique-scannr           ✓              
min-mod-mass            ✓             
c-neg              ✓✓          
c-pos              ✓✓          
decoy-xml-output              ✓✓          
default-direction              ✓✓          
feature-file-out              ✓✓          
fido-alpha              ✓✓          
fido-beta              ✓✓          
fido-empirical-protein-q              ✓✓          
fido-fast-gridsearch              ✓✓          
fido-gamma              ✓✓          
fido-gridsearch-depth              ✓✓          
fido-gridsearch-mse-threshold              ✓✓          
fido-no-split-large-components              ✓✓          
fido-protein-truncation-threshold              ✓✓          
init-weights              ✓✓          
klammer              ✓✓          
maxiter              ✓✓          
no-terminate              ✓✓          
only-psms              ✓✓          
output-weights              ✓✓          
override              ✓✓          
percolator-seed              ✓✓          
picked-protein              ✓✓          
pout-output              ✓✓          
protein              ✓✓          
protein-enzyme              ✓✓          
protein-report-duplicates              ✓✓          
protein-report-fragments              ✓✓          
protein-name-separator              ✓✓          
quick-validation              ✓✓          
search-input              ✓✓          
spectral-counting-fdr              ✓✓          
static              ✓✓          
subset-max-train              ✓✓          
tdc              ✓✓          
test-each-iteration              ✓✓          
test-fdr              ✓✓          
train-best-positive              ✓✓          
train-fdr              ✓✓          
unitnorm              ✓✓          
bullseye               ✓          
search-engine               ✓          
post-processor               ✓          
allow-dups               ✓      ✓   
cterm-protein-mods-spec               ✓      ✓   
max-mods               ✓      ✓   
memory-limit               ✓      ✓   
min-mods               ✓      ✓   
nterm-protein-mods-spec               ✓      ✓   
auto-modifications               ✓      ✓   
auto-modifications-spectra               ✓      ✓   
num-decoys-per-target               ✓      ✓   
peptide-list               ✓     ✓✓   
temp-dir               ✓      ✓   
parsimony               ✓    ✓     
threshold               ✓    ✓     
threshold-type               ✓    ✓     
input-ms2               ✓    ✓     
unique-mapping               ✓    ✓     
quant-level               ✓    ✓     
measure               ✓    ✓     
custom-threshold-name               ✓    ✓     
custom-threshold-min               ✓    ✓     
mzid-use-pass-threshold               ✓    ✓     
protein-database               ✓  ✓ ✓     
primary-ions                ✓         
precursor-ions                ✓         
isotope                ✓         
flanking                ✓         
max-ion-charge                ✓         
fragment-mass                ✓         
nh3                ✓         
h2o                ✓         
stop-after                 ✓        
output-units                 ✓        
input-format                  ✓       
distinct-matches                  ✓       
predrt-files                        ✓ 
prec-ppm                        ✓ 
frag-ppm                        ✓ 
diameter-instrument                        ✓ 
spectrum-outdir                         ✓