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SiprosConfig.cfg
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###########################################################
##### Parameters for peptide identification by Sipros #####
###########################################################
[Peptide_Identification]
# Search_Name is inserted to the output filename. Use "Null" to insert nothing
Search_Name = SE
# Search_Type Options: "Regular", "Mutation", "SIP"
Search_Type = Regular
# Filename of the FASTA database
FASTA_Database = ./toy_example/human_gut_fiber_V2_Rev.fasta
# Fragmentation method: currently only considers CID and HCD
Fragmentation_Method = HCD
##### Mass_Accuracy #####
# Mass Windows to be open around parent ion. -->
# Examples: a center window: "0", a center window and an offset window: "-1,0", etc -->
Parent_Mass_Windows = -1, 0, 1, 2, 3
# Parent mass tolerance for database searching
# Recommend 1 Da for both High-res MS2 and Low-res MS2 to improve identification results
# Peptides with large errors for parent ions can be filtered out using the parameter Filter_Mass_Tolerance_Parent_Ion
Search_Mass_Tolerance_Parent_Ion = 1
# Fragment mass tolerance: e.g. "0.05" for High-res MS2 and "0.5" for Low-res MS2. -->
Mass_Tolerance_Fragment_Ions = 0.05
# Minimum and maximum length of peptides to be generated from in silico digestion
Minimum_Peptide_Length = 4
Maximum_Peptide_Length = 101
##### Rules for in silico digestion #####
# Cleave after these residues
Cleave_After_Residues = KR
# Cleave before these residues
Cleave_Before_Residues = ACDEFGHIJKLMNPQRSTVWY
# Maximum number of missed cleavages in a peptide
Maximum_Missed_Cleavages = 3
# Try removing the first methionine in a protein
Try_First_Methionine = true
##### PTM identification #####
# Maximum number of PTMs considered for a peptide
Max_PTM_Count = 1
PTM{~} = M # Oxidation of Met
#PTM{!} = NQ # Deamidation of NQ
#PTM{@} = STYHD # Phosphorylation
#PTM{>to1} = STYHD # Phosphorylation with losing HPO3
#PTM{<to2} = ST # Phosphorylation with losing HPO3 and H2O
#PTM{%} = K # Acetylation
#PTM{^} = KRED # Mono-methylation
#PTM{&} = KR # Di-methylation
#PTM{*} = K # Tri-methylation
#PTM{(} = C # S-Nitrosylation, search with natural Cys
#PTM{)} = Y # Nitration
#PTM{/} = C # IAA blocking
#PTM{$} = D # beta-methylthiolation
##### Elemental composition of amino acid residues #####
Element_List = C, H, O, N, P, S
Residue{Nterm} = 0, 1, 0, 0, 0, 0 # N terminus
Residue{Cterm} = 0, 1, 1, 0, 0, 0 # C terminus
Residue{J} = 6, 11, 1, 1, 0, 0 # J is I or L
Residue{I} = 6, 11, 1, 1, 0, 0
Residue{L} = 6, 11, 1, 1, 0, 0
Residue{A} = 3, 5, 1, 1, 0, 0
Residue{S} = 3, 5, 2, 1, 0, 0
Residue{G} = 2, 3, 1, 1, 0, 0
Residue{V} = 5, 9, 1, 1, 0, 0
Residue{E} = 5, 7, 3, 1, 0, 0
Residue{K} = 6, 12, 1, 2, 0, 0
Residue{T} = 4, 7, 2, 1, 0, 0
Residue{D} = 4, 5, 3, 1, 0, 0
Residue{R} = 6, 12, 1, 4, 0, 0
Residue{P} = 5, 7, 1, 1, 0, 0
Residue{N} = 4, 6, 2, 2, 0, 0
Residue{F} = 9, 9, 1, 1, 0, 0
Residue{Q} = 5, 8, 2, 2, 0, 0
Residue{Y} = 9, 9, 2, 1, 0, 0
Residue{M} = 5, 9, 1, 1, 0, 1
Residue{H} = 6, 7, 1, 3, 0, 0
Residue{C} = 5, 8, 2, 2, 0, 1 # Blocked Cys by IAA
#Residue{C} = 3, 5, 1, 1, 0, 1 # Natural Cys
Residue{W} = 11, 10, 1, 2, 0, 0
Residue{~} = 0, 0, 1, 0, 0, 0, # Oxidation or Hydroxylation
Residue{!} = 0, -1, 1, -1, 0, 0, # Deamidation or Citrullination if happens at Arg
#Residue{@} = 0, 1, 3, 0, 1, 0, # Phosphorylation
#Residue{>} = 0, 1, 3, 0, 1, 0, # Phosphorylation
#Residue{<} = 0, 1, 3, 0, 1, 0, # Phosphorylation
#Residue{1} = 0, 0, 0, 0, 0, 0, # Phosphorylation with losing HPO3
#Residue{2} = 0, -2, -1, 0, 0, 0, # Phosphorylation with losing HPO3 and H2O
#Residue{%} = 2, 2, 1, 0, 0, 0, # Acetylation
#Residue{^} = 1, 2, 0, 0, 0, 0, # Mono-methylation
#Residue{&} = 2, 4, 0, 0, 0, 0, # Di-methylation
#Residue{*} = 3, 6, 0, 0, 0, 0, # Tri-methylation
#Residue{(} = 0, -1, 1, 1, 0, 0, # S-Nitrosylation
#Residue{)} = 0, -1, 2, 1, 0, 0, # Nitration
#Residue{/} = 2, 3, 1, 1, 0, 0, # IAA blocking
#Residue{$} = 1, 2, 0, 0, 0, 1, # beta-methylthiolation
##### Isotopic distribution of elements #####
# Carbon
Element_Masses{C} = 12.000000, 13.003355
Element_Percent{C} = 0.9893, 0.0107
# Hydrogen
Element_Masses{H} = 1.007825, 2.014102
Element_Percent{H} = 0.999885, 0.000115
# Oxygen
Element_Masses{O} = 15.994915, 16.999132, 17.999160
Element_Percent{O} = 0.99757, 0.00038, 0.00205
# Nitrogen
Element_Masses{N} = 14.003074, 15.000109
Element_Percent{N} = 0.99632, 0.00368
# Phosphorus
Element_Masses{P} = 30.973762
Element_Percent{P} = 1.0
# Sulfur
Element_Masses{S} = 31.972071, 32.971459, 33.967867, 34.967867, 35.967081
Element_Percent{S} = 0.9493, 0.0076, 0.0429, 0.0000, 0.0002
###########################################################
##### Parameters for protein identification by Sipros #####
###########################################################
[Protein_Identification]
# the prefix of training decoy sequences' locus IDs in the database
Training_Decoy_Prefix = Rev_
# the prefix of testing decoy sequences' locus IDs in the database
Testing_Decoy_Prefix = Rev_
# Level of FDR filtering. Options: "PSM" and "Peptide"
FDR_Filtering = Peptide
# FDR threshold for filtering peptide identifications -->
FDR_Threshold = 0.01
# Minimum number of peptides per protein -->
Min_Peptide_Per_Protein = 1
# Minimum number of unique peptides per protein
Min_Unique_Peptide_Per_Protein = 1
# Parent mass tolerance: e.g. "0.05" for High-res MS1 and "3" for Low-res MS1, default unit is Da
Filter_Mass_Tolerance_Parent_Ion = 0.05
# Atomic mass error unit, either "PPM" or "Da"
Filter_Mass_Tolerance_Parent_Ion_Unit = Da