Vseq.ini

[Parameters]
# General
min_dm = 3				# Min. deltamass value required to consider a peptide as modified
min_ions_matched = 2			# Min. number of matched ions required in a candidate
precursor_tolerance = 0.3		# Tolerance in Th (To match ExpNeutralMass to m/z values in mgf)
fragment_tolerance = 15			# Tolerance in ppm (Max. ppm error)
intensity_percent_threshold = 0.01	# Remove peaks from MS2 spectra whose intensity is below this % of the maximum intensity.
ppm_plot = 30				# Max. ppm error for fragments in the interpreted plot

# ScanIntegrator
int_scanrange = 6			# ± Number of MS1 (full) scans to integrate
int_mzrange = 2				# m/z range to integrate for
int_binwidth = 0.001			# Bin width to integrate with
int_matchwidth = 4			# ± Bins to match experimental and theoretical isotopic envelopes
poisson_threshold = 0.8			# % coverage of isotopic envelope to reach with theoretical peaks
expected_variance = 0.005		# Expected variance for a good theoretical-experimental distribution match

# VSeqExplorer
best_n = 5				# Number of candidates to make Vseq plots for
sort_by = hyperscore			# Criterion to sort candidates by (Options = ions_matched, e_score, product, v_score, hyperscore)
vseq_threshold = 10			# Min. value to plot VseqExplorer results
parallelize = peptide			# Criterion to parallelize by (Options = peptide, protein, both)
diagnostic_ions = 3			# Diagnostic ions to use per fragmentation series, from this ion to the end of each sequence
keep_n = 15				# Keep the first n spectra sorted by sum of diagnostic ions intensity

[Aminoacids]
A = 71.037114
R = 156.101111
N = 114.042927
D = 115.026943
C = 103.009185
E = 129.042593
Q = 128.058578
G = 57.021464
H = 137.058912
I = 113.084064
L = 113.084064
K = 128.094963
M = 131.040485
F = 147.068414
P = 97.052764
S = 87.032028
T = 101.047679
U = 150.953630
W = 186.079313
Y = 163.063329
V = 99.068414
O = 132.089878
Z = 129.042594

[Fixed Modifications]
Nt = 0         
Ct = 0
A = 0
R = 0
N = 0
D = 0
C = 0 # Carbamidomethyl = 57.021464 
E = 0
Q = 0
G = 0
H = 0
I = 0
L = 0
K = 0           
M = 0
F = 0
P = 0
S = 0
T = 0
U = 0
W = 0
Y = 0
V = 0
O = 0

[Masses]
m_proton = 1.007276
m_hydrogen = 1.007825
m_oxygen = 15.994915

[Logging]
create_log = 1		# Create log file, 0=no 1=yes
create_ini = 0		# Create copy of INI file in input directory, 0=no 1=yes (specifying custom parameters in the command line will always create a copy of INI file)