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search# mgf_file enzyme mcs database mods
synthetic_siRNA_Waters_Q-Tof_MaxEnt3 noEnzyme.txt 0 siRNA(UUCUGUAAUCUCUUGUCUA(dT)(dT)) 0
150625_RNAanti_100fmol_NCE15_spice13 noEnzyme.txt 0 siRNA(AGUAGUUGGCAUAGGAGUC(dT)(dT)) 0
150625_DNA6mix_100fmol_NCE20_spice13 noEnzyme.txt 0 dna6mix 0
141203_c25S_5dU_50f_spice11_20160712 RNaseT1.txt 0 S_cerevisiae/rRNA 2
160427tRNAphe50f04_spice11 RNaseT1.txt 2 Sc_tRNA_modomics 4
160427tRNAphe50f04_spice11 RNaseT1.txt 2 Sc_tRNA_site_direct_mod 0
human_smallRNA_fraction RNaseT1.txt 0 H_sapiens 0
131106hela-miRNA12-27_spice11 noEnzyme.txt 0 H_sapiens/miRNA_var 0

Examples: mgf, fasta and mods

mgf sequence without modification sequence with modification modification file parameters
131106hela-miRNA12-27_spice11.mgf H_sapiens_miRNA_var.fasta - - 131106hela-miRNA12-27_spice11.txt
141203_c25S_5dU_50f_spice11.mgf S_cerevisiae_rRNA.fasta - Sce_25S_rRNA_partial.mods 141203_c25S_5dU_50f_spice11.txt
160427tRNAphe50f04_spice11.mgf - Sc_tRNA_site_direct_mod.fasta - 160427tRNAphe50f04_spice11.txt

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