| assign-confidence | barista | cascade-search | comet | create-docs | bullseye | hardklor | extract-columns | extract-rows | generate-peptides | get-ms2-spectrum | make-pin | localize-modification | param-medic | percolator | pipeline | predict-peptide-ions | print-processed-spectra | psm-convert | q-ranker | read-tide-index | search-for-xlinks | sort-by-column | spectral-counts | stat-column | subtract-index | tide-index | tide-search | xlink-assign-ions | xlink-score-spectrum |
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 | ✓ | ✓ | ✓ | ✓ | | ✓ | ✓ | | | ✓ | | ✓ | | | ✓ | ✓ | | | | ✓ | | | | ✓ | | | | ✓ | | |
enzyme | | ✓ | | | | | | | | ✓ | | | | | | | | | | ✓ | | ✓ | | | | | ✓ | | | |
separate-searches | | ✓ | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | |
pepxml-output | | ✓ | ✓ | | | | | | | | | | | | ✓ | ✓ | | | | ✓ | | | | | | | | ✓ | | |
txt-output | | ✓ | ✓ | | | | | | | | | | | | ✓ | ✓ | | | | ✓ | | | | | | | | ✓ | | |
skip-cleanup | | ✓ | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | |
re-run | | ✓ | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | |
use-spec-features | | ✓ | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | |
feature-file-out | | ✓ | | | | | | | | | | | | | ✓ | ✓ | | | | ✓ | | | | | | | | | | |
optimization | | ✓ | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
spectrum-parser | | ✓ | ✓ | | | | | | | | ✓ | | | ✓ | | ✓ | | ✓ | | ✓ | | ✓ | | ✓ | | | | ✓ | ✓ | |
q-value-threshold | | | ✓ | | | | | | | | | | | | | | | | | | | | | | | | | | | |
auto-mz-bin-width | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
auto-precursor-window | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
compute-sp | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
concat | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
deisotope | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
exact-p-value | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
file-column | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
isotope-error | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
mass-precision | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | ✓ | ✓ | ✓ | | |
max-precursor-charge | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
min-peaks | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
mod-precision | | | ✓ | | | | | | | ✓ | | | ✓ | | | ✓ | | | | | | ✓ | | | | | ✓ | ✓ | | |
mz-bin-offset | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
mz-bin-width | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | ✓ | |
mzid-output | | | ✓ | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | ✓ | | |
num-threads | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
peptide-centric-search | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
score-function | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
fragment-tolerance | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
evidence-granularity | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
pin-output | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
pm-charge | | | ✓ | ✓ | | | | | | | | | | ✓ | | ✓ | | | | | | | | | | | | ✓ | | |
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 | | | ✓ | | | | | | | | ✓ | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
skip-preprocessing | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
spectrum-charge | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
spectrum-max-mz | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
spectrum-min-mz | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | |
sqt-output | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
store-index | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
store-spectra | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
use-flanking-peaks | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | ✓ | | | | | | ✓ | | ✓ |
use-neutral-loss-peaks | | | ✓ | | | | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | |
use-z-line | | | ✓ | | | | | | | | ✓ | | | | | ✓ | | ✓ | | | | ✓ | | | | | | ✓ | | |
decoy_search | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
num_threads | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
peptide_mass_tolerance | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
auto_peptide_mass_tolerance | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
peptide_mass_units | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
mass_type_parent | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
mass_type_fragment | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
precursor_tolerance_type | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
isotope_error | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
search_enzyme_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_NL_ions | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_sqtfile | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_txtfile | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_pepxmlfile | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_percolatorfile | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_outfiles | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
print_expect_score | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
num_output_lines | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
show_fragment_ions | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
sample_enzyme_number | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
scan_range | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
precursor_charge | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
override_charge | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
ms_level | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
activation_method | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
digest_mass_range | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
num_results | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
skip_researching | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
max_fragment_charge | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
max_precursor_charge | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
nucleotide_reading_frame | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
clip_nterm_methionine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
spectrum_batch_size | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
decoy_prefix | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
output_suffix | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
mass_offsets | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
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 | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
max_variable_mods_in_peptide | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
require_variable_mod | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Cterm_peptide | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Nterm_peptide | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Cterm_protein | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Nterm_protein | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_A_alanine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_B_user_amino_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_C_cysteine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_D_aspartic_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_E_glutamic_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_F_phenylalanine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_G_glycine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_H_histidine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_I_isoleucine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_J_user_amino_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_K_lysine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_L_leucine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_M_methionine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_N_asparagine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_O_ornithine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
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_X_user_amino_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Y_tyrosine | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
add_Z_user_amino_acid | | | | ✓ | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
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 | | | | | | | ✓ | | | | | | | | | | | | | | | | | | | | | | | |
delimiter | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | ✓ | | ✓ | | | | | |
header | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | ✓ | | ✓ | | | | | |
comparison | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | | | | | |
column-type | | | | | | | | | ✓ | | | | | | | | | | | | | | ✓ | | | | | | | |
min-mass | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
max-mass | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
min-length | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
max-length | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
custom-enzyme | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
digestion | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
missed-cleavages | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
isotopic-mass | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
seed | | | | | | | | | | ✓ | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
clip-nterm-methionine | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | ✓ | | | |
decoy-format | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | ✓ | | | |
keep-terminal-aminos | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | ✓ | | | |
stats | | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | | | |
max-charge-feature | | | | | | | | | | | | ✓ | | | ✓ | ✓ | | | | | | | | | | | | | | |
output-file | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | | |
top-match | | | | | | | | | | | | ✓ | ✓ | | ✓ | ✓ | | | | | | ✓ | | | | | | ✓ | | |
min-mod-mass | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | | | | |
c-neg | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
c-pos | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
decoy-xml-output | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
default-direction | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
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 | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
only-psms | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
output-weights | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
override | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
percolator-seed | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
picked-protein | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
pout-output | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
protein | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
protein-enzyme | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
protein-report-duplicates | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
protein-report-fragments | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
quick-validation | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
search-input | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
spectral-counting-fdr | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
subset-max-train | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
tdc | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
test-each-iteration | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
test-fdr | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
train-best-positive | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
train-fdr | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
unitnorm | | | | | | | | | | | | | | | ✓ | ✓ | | | | | | | | | | | | | | |
bullseye | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
search-engine | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
post-processor | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | | |
primary-ions | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
precursor-ions | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
isotope | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
flanking | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
max-ion-charge | | | | | | | | | | | | | | | | | ✓ | | | | | ✓ | | | | | | | ✓ | |
fragment-mass | | | | | | | | | | | | | | | | | ✓ | | | | | ✓ | | | | | | | ✓ | |
nh3 | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
h2o | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | | |
stop-after | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | |
output-units | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | | |
input-format | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | |
distinct-matches | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | | | | |
protein-database | | | | | | | | | | | | | | | | | | | ✓ | | | | | ✓ | | | | | | |
use-old-xlink | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-linears | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-deadends | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-selfloops | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-inter | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-intra | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-include-inter-intra | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-prevents-cleavage | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
require-xlink-candidate | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
xlink-top-n | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
max-xlink-mods | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
mods-spec | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
cmod | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
nmod | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
max-mods | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | ✓ | | | |
mono-link | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
precursor-window-weibull | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
precursor-window-type-weibull | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
min-weibull-points | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
use-a-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
use-b-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
use-c-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
use-x-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
use-y-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
use-z-ions | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | ✓ |
mod-mass-format | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
isotope-windows | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
compute-p-values | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | | |
ascending | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | | |
parsimony | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
threshold | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
threshold-type | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
input-ms2 | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
unique-mapping | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
quant-level | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
measure | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
custom-threshold-name | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
custom-threshold-min | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
mzid-use-pass-threshold | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | | | | |
peptide-list | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | ✓ | | | |
allow-dups | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | |
cterm-peptide-mods-spec | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | |
min-mods | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | |
nterm-peptide-mods-spec | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | |
temp-dir | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ | | | |
xlink-score-method | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ✓ |