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parameter.txt
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parameter.txt
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# database search parameter setting
database ecoli_riboprot_fwdanddec.fasta # protein sequence database
MS_data_directory /u/jic/crosslink/python/mzxml/ # absolute path of directory containing spectra files
XLresidue K # aa residue to be linked
ms1tol_unit ppm # ms1 tolerance unit
ms1tol_val 5 # ms1 tolerance value
ms2tol_unit da # ms2 tolerance unit
ms2tol_val 0.01 # ms2 tolerance value
linker_mass 136.10005 # mass of cross-linker
miss_cleave 2 # maximum miss cleavages per peptide
min_peplen 4 # mininum peptide length
max_peplen 51 # max peptide length
fix_mod_res C # fixed modification residue, e.g. 'C'
fix_mod_mass 57.02146 # delta mass of fixed modification, e.g. '57.02146'
var_mod_res # variable modification residue, e.g. 'O'
var_mod_mass 0 # delta mass of variable modification, e.g. '15.99'
ntermxlink False # nterm cross-linkable
# theoretical spectrum setting
min_preXL_ions_ch 1 # minimum charge of theoretical ions not containing cross-linker
max_preXL_ions_ch 3 # maximum charge of theoretical ions not containing cross-linker
min_postXL_ions_ch 2 # minimum charge of theoretical ions containing cross-linker
max_postXL_ions_ch 5 # maximum charge of theoretical ions containing cross-linker
include_a_ions True # consider A ions or not for matching
max_iterations 10 # max iterations of the iterative procedure that estimates class priors
annotate_spec False # annotate PSM or not
# applicable only in training mode
target_database ecoli_riboprot.fasta
uniprot_database uniprot_sprot.fasta
# Classifier I (TT-TF) coefficients
CI00 -9.756727002663403425231081200763583183288574218750000000000000
CI01 0.062319747953648044203056599599221954122185707092285156250000
CI02 -0.169152908780707156299882854000316001474857330322265625000000
CI03 4.092302681977518119538217433728277683258056640625000000000000
CI04 -0.087049551483903420123766636606887914240360260009765625000000
CI05 0.004029467231824575279564015772848506458103656768798828125000
CI06 3.813704426312439110802188224624842405319213867187500000000000
CI07 -0.121262329798635257183114788404054706916213035583496093750000
CI08 0.103075396608244662655096135495114140212535858154296875000000
CI09 0.923755177680745442891918628447456285357475280761718750000000
CI10 1.241437135116305601201247554854489862918853759765625000000000
CI11 5.397481875886480651161036803387105464935302734375000000000000
CI12 -0.489090661683284910754565544266370125114917755126953125000000
CI13 0.240261064016898701067859178692742716521024703979492187500000
CI14 9.236944094043588293629909458104521036148071289062500000000000
CI15 -1.379131846229504798628795469994656741619110107421875000000000
CI16 -0.207531323320800153986454006371786817908287048339843750000000
# Classifier II (TF-FF) coefficients
CII00 -10.144797654825151056456888909451663494110107421875000000000000
CII01 0.481045588861673756309045302259619347751140594482421875000000
CII02 0.542839766583352756335045796731719747185707092285156250000000
CII03 8.433926381962203677744582819286733865737915039062500000000000
CII04 -0.257086429727803544853514949863892979919910430908203125000000
CII05 0.369264868819644598296747517451876774430274963378906250000000
CII06 23.649986303785432539825706044211983680725097656250000000000000
CII07 1.814813008476831246440497125149704515933990478515625000000000
CII08 -0.226694828051599767126944584560988005250692367553710937500000
CII09 -0.027532917890448573017270206264583976007997989654541015625000
CII10 0.010068626511572332030142185033128043869510293006896972656250
CII11 6.709811790635387573900061397580429911613464355468750000000000
CII12 -0.012404347781189151156411298870807513594627380371093750000000
CII13 -0.124072317582141433689457699074409902095794677734375000000000
CII14 17.851597701633423298517300281673669815063476562500000000000000
CII15 1.543070862970395085156383174762595444917678833007812500000000
CII16 0.059029394544471140704455791592408786527812480926513671875000
#
nTT 169
nTF 8568
nFF 91242