#PMi-Byonic parameters v1.4.1
#Registered to: Hirokazu Yagi Nagoya City Univercity Graduate School of Pharmaceautical Sciences
#Build info: v5.7.11-gab350a33 -- release/2024.09 (Fri 09/27/2024 08:28 AM); Demo
#Java version: 1.8.0_371
#Java home: C:\Program Files\Java\jre-1.8
#OS Arch: amd64
#OS Name: Windows 11
#OS Version: 10.0
#
#Thu Jan 09 11:48:48 JST 2025
apply_charges_text=
skip_bad_spectra=1
n_glycan_checkbox=0
lock_mass_list=None
DatabaseFiles=D\:\\Tardigrate.fasta
Custom_xlink=0
common_max=2
results_suffix=220809Tardigrate v2
peak_filter_min_number=0
ProteomeDiscovererVersion=
fragment_mass_error=10.0
DSS_xlink=0
DebugMode=0
random_sample_size=400
export_mzIdentML_checkbox=1
min_chunk_size=500
combyne_auto_score=1
precursor_mass_max=10000.0
max_chunk_size=2000
peak_filter_selected=\n
output_results=1
off_by_one=3
peak_filter_rank_cutoff=50
machine_type=ma\:ftms, ma\:itms
recal_coeffs=
msconvert_filter=
wildcard_residues=
max_precursors=1
rare_max=1
score_version=2
DebugText=
add_decoys=1
precursor_mass_error=5.0
glycan_text=% N-glycan 38 insect.txt\nHexNAc(1) @ NGlycan | rare1\nHexNAc(2) @ NGlycan | rare1\nHexNAc(1)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(1) @ NGlycan | rare1\nHexNAc(2)Hex(1)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(2) @ NGlycan | rare1\nHexNAc(2)Hex(2)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(3) @ NGlycan | rare1\nHexNAc(2)Hex(3)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(4) @ NGlycan | rare1\nHexNAc(2)Hex(4)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(5) @ NGlycan | rare1\nHexNAc(2)Hex(5)Fuc(1) @ NGlycan | rare1\nHexNAc(2)Hex(6) @ NGlycan | rare1\nHexNAc(2)Hex(7) @ NGlycan | rare1\nHexNAc(2)Hex(8) @ NGlycan | rare1\nHexNAc(2)Hex(9) @ NGlycan | rare1\nHexNAc(2)Hex(10) @ NGlycan | rare1\nHexNAc(2)Hex(11) @ NGlycan | rare1\nHexNAc(1)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(1)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(2)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(3)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(4)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(5)Fuc(2) @ NGlycan | rare1\nHexNAc(3)Hex(3) @ NGlycan | rare1\nHexNAc(3)Hex(3)Fuc(1) @ NGlycan | rare1\nHexNAc(3)Hex(3)Fuc(2) @ NGlycan | rare1\nHexNAc(3)Hex(4) @ NGlycan | rare1\nHexNAc(3)Hex(4)Fuc(1) @ NGlycan | rare1\nHexNAc(3)Hex(4)Fuc(2) @ NGlycan | rare1\nHexNAc(3)Hex(5) @ NGlycan | rare1\nHexNAc(3)Hex(5)Fuc(1) @ NGlycan | rare1\nHexNAc(3)Hex(5)Fuc(2) @ NGlycan | rare1\nHexNAc(4)Hex(3) @ NGlycan | rare1\nHexNAc(4)Hex(3)Fuc(1) @ NGlycan | rare1\nHexNAc(4)Hex(3)Fuc(3) @ NGlycan | rare1\nHexNAc(4)Hex(3)Fuc(2) @ NGlycan | rare1\nHexNAc(2)Hex(3)Fuc(1) @ NGlycan | rare1\nHexNAc(5)Hex(3)Fuc(2) @ NGlycan | rare1\nHexNAc(4)Hex(3)Fuc(2)  @ NGlycan | rare1\n% Custom modification text below\n\n
nglycan_quick_reject_labile_scale=0.01
Wildcard=0
maximum_missed_cleavages=2
extra_text=
xlink_decoys_checkbox=0
deisotoped_spectra_checkbox=0
chunking_method=2
DigestLetters=RK
PARAMETER_VERSION=1.4.1
peak_filter_mz_tolerance=0.02
output_top_scores=0
combyne_min_score=-100
inclusion_filter=StartMz,EndMz,StartTime,EndTime
precursor_unit=0
mod_text=Carbamidomethyl / +57.021464 @ C | fixed\nOxidation / +15.994915 @ M | common1\n% Custom modification text below\n
combyne_fdr=
OutputFolder=D\:\\Bionic
Trisulfide_text=Trisulfide / 29.956421 @ C | xlink
enable_promote_score_nglycan=0
apply_charges_index=1
precursor_ppm_hardcut=0
add_contaminants=0
DSS_xlink_text=DSS / 138.0680796 @ K | xlink\nXlink\:DSS / 156.078644 @ K | common2 % Dead end
centroid_prefer_type=2
recal_option=0
combyne_extra_params=
protein_fdr_pulldown=0
centroid_width_type=0
quick_reject_wildcard=99.0
disulfide_protein_groups=1
precursor_assignments=1
xlink_details=
wildcard_delta=0
DigestCutterType=0
centroid_width_val=0.01
Disulfide=0
quick_reject=95.0
Custom_xlink_text=
wildcard_max_mass=55
o_glycan_checkbox=0
fragment_ppm_hardcut=0
features_text=
Disulfide_text=Disulfide / -2.015650 @ C | xlink
fragment_unit2=0
Trisulfide=0
wildcard_min_mass=45
xlink_decoys_mass_offset=11
centroid_topk=1000
SpectraFiles=D\:\\Raw\\20200324_kuma64_GlycoProteome\\20200324_kuma64_glycoPepConc_Inj10uL_01.raw
focused_database_checkbox=0
DigestType=2
fragment_mass_error2=20.0
fragment_unit=0
output_report=0