Hello, It seems that your issue may be caused by this parameter: ms_level = 2-3 # MS level to analyze, valid are levels 2 (default) or 3 Please specify it as a single value, e.g. ms_level = *3* # MS level to analyze, valid are levels 2 (default) or 3
Hope this helps, --Luis On Fri, Jul 15, 2022 at 9:17 AM Aarthie Senathirajah < animallover....@gmail.com> wrote: > Hi > I'm currently having an issue with comet in TPP where I use my MZXML file > and when I set my comet params mslevel= 3 it does not load any spectra. > > I've check the mzxml file and it does contain MS3 spectra so I'm not sure > why this is occurring. Here is a copy of my comet params file . > # comet_version 2018.01 rev. 4 > # Generated via Petunia/TPP by guest on Fri Jul 15 11:43:46 2022 > # Comet MS/MS search engine parameters file. > # Everything following the '#' symbol is treated as a comment. > > database_name = /some/path/db.fasta > decoy_search = 1 # 0=no (default), 1=concatenated > search, 2=separate search > peff_format = 0 # 0=no (normal fasta, default), > 1=PEFF PSI-MOD, 2=PEFF Unimod > peff_obo = # path to PSI Mod or Unimod OBO file > > num_threads = 0 # 0=poll CPU to set num threads; > else specify num threads directly (max 128) > > # > # masses > # > peptide_mass_tolerance = 50.00 > peptide_mass_units = 2 # 0=amu, 1=mmu, 2=ppm > mass_type_parent = 1 # 0=average masses, 1=monoisotopic > masses > mass_type_fragment = 1 # 0=average masses, 1=monoisotopic > masses > precursor_tolerance_type = 1 # 0=MH+ (default), 1=precursor m/z; > only valid for amu/mmu tolerances > isotope_error = 3 # 0=off, 1=0/1 (C13 error), > 2=0/1/2, 3=0/1/2/3, 4=-8/-4/0/4/8 (for +4/+8 labeling) > > # > # search enzyme > # > search_enzyme_number = 1 # choose from list at end of this > params file > num_enzyme_termini = 2 # 1 (semi-digested), 2 (fully > digested, default), 8 C-term unspecific , 9 N-term unspecific > allowed_missed_cleavage = 2 # maximum value is 5; for enzyme > search > > # > # Up to 9 variable modifications are supported > # format: <mass> <residues> <0=variable/else binary> > <max_mods_per_peptide> <term_distance> <n/c-term> <required> > # e.g. 79.966331 STY 0 3 -1 0 0 > # > variable_mod01 = 15.9949 M 0 3 -1 0 0 > variable_mod02 = 0.0 X 0 3 -1 0 0 > variable_mod03 = 0.0 X 0 3 -1 0 0 > variable_mod04 = 0.0 X 0 3 -1 0 0 > variable_mod05 = 0.0 X 0 3 -1 0 0 > variable_mod06 = 0.0 X 0 3 -1 0 0 > variable_mod07 = 0.0 X 0 3 -1 0 0 > variable_mod08 = 0.0 X 0 3 -1 0 0 > variable_mod09 = 0.0 X 0 3 -1 0 0 > max_variable_mods_in_peptide = 5 > require_variable_mod = 0 > > # > # fragment ions > # > # ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), > theoretical_fragment_ions = 1 > # high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), > theoretical_fragment_ions = 0, spectrum_batch_size = 10000 > # > fragment_bin_tol = 1.0005 # binning to use on fragment ions > fragment_bin_offset = 0.4 # offset position to start the > binning (0.0 to 1.0) > theoretical_fragment_ions = 1 # 0=use flanking peaks, 1=M peak > only > use_A_ions = 0 > use_B_ions = 1 > use_C_ions = 0 > use_X_ions = 0 > use_Y_ions = 1 > use_Z_ions = 0 > use_NL_ions = 0 # 0=no, 1=yes to consider NH3/H2O > neutral loss peaks > > # > # output > # > output_sqtstream = 0 # 0=no, 1=yes write sqt to > standard output > output_sqtfile = 0 # 0=no, 1=yes write sqt file > output_txtfile = 0 # 0=no, 1=yes write tab-delimited > txt file > output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file > output_percolatorfile = 0 # 0=no, 1=yes write Percolator > tab-delimited input file > print_expect_score = 1 # 0=no, 1=yes to replace Sp with > expect in out & sqt > num_output_lines = 5 # num peptide results to show > show_fragment_ions = 0 # 0=no, 1=yes for out files only > > sample_enzyme_number = 1 # Sample enzyme which is possibly > different than the one applied to the search. > # Used to calculate NTT & NMC in > pepXML output (default=1 for trypsin). > > # > # mzXML parameters > # > scan_range = 0 0 # start and end scan range to > search; either entry can be set independently > precursor_charge = 0 0 # precursor charge range to > analyze; does not override any existing charge; 0 as 1st entry ignores > parameter > override_charge = 0 # 0=no, 1=override precursor charge > states, 2=ignore precursor charges outside precursor_charge range, 3=see > online > ms_level = 2-3 # MS level to analyze, valid are > levels 2 (default) or 3 > activation_method = CID # activation method; used if > activation method set; allowed ALL, CID, ECD, ETD, ETD+SA, PQD, HCD, IRMPD > > # > # misc parameters > # > digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze > num_results = 100 # number of search hits to store > internally > skip_researching = 1 # for '.out' file output only, > 0=search everything again (default), 1=don't search if .out exists > max_fragment_charge = 3 # set maximum fragment charge state > to analyze (allowed max 5) > max_precursor_charge = 6 # set maximum precursor charge > state to analyze (allowed max 9) > nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward > three, 8=reverse three, 9=all six > clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also > consider sequence w/o N-term methionine > spectrum_batch_size = 0 # max. # of spectra to search at a > time; 0 to search the entire scan range in one loop > decoy_prefix = DECOY_ # decoy entries are denoted by this > string which is pre-pended to each protein accession > equal_I_and_L = 1 # 0=treat I and L as different; > 1=treat I and L as same > output_suffix = # add a suffix to output base names > i.e. suffix "-C" generates base-C.pep.xml from base.mzXML input > mass_offsets = # one or more mass offsets to > search (values substracted from deconvoluted precursor mass) > > # > # spectral processing > # > minimum_peaks = 10 # required minimum number of peaks > in spectrum to search (default 10) > minimum_intensity = 0 # minimum intensity value to read in > remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced > precursor peaks (for ETD), 3=phosphate neutral loss peaks > remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor > removal > clear_mz_range = 125.5 131.5 # for iTRAQ/TMT type data; will > clear out all peaks in the specified m/z range # > > # > # additional modifications > # > > add_Cterm_peptide = 0.0 > add_Nterm_peptide = 229.1629 > add_Cterm_protein = 0.0 > add_Nterm_protein = 0.0 > > add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. > 57.02146 > add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. > 71.03711 > add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. > 87.03203 > add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. > 97.05276 > add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. > 99.06841 > add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. > 101.04768 > add_C_cysteine = 57.021464 # added to C - avg. 103.1429, mono. > 103.00918 > add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. > 113.08406 > add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. > 113.08406 > add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. > 114.04293 > add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. > 115.02694 > add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. > 128.05858 > add_K_lysine = 229.1629 # added to K - avg. 128.1723, > mono. 128.09496 > add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. > 129.04259 > add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. > 131.04048 > add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono > 132.08988 > add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. > 137.05891 > add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. > 147.06841 > add_U_selenocysteine = 0.0000 # added to U - avg. 150.0379, mono. > 150.95363 > add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. > 156.10111 > add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. > 163.06333 > add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. > 186.07931 > add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. > 0.00000 > add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. > 0.00000 > add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. > 0.00000 > add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. > 0.00000 > > # > # COMET_ENZYME_INFO _must_ be at the end of this parameters file > # > [COMET_ENZYME_INFO] > 0. No_enzyme 0 - - > 1. Trypsin 1 KR P > 2. Trypsin/P 1 KR - > 3. Lys_C 1 K P > 4. Lys_N 0 K - > 5. Arg_C 1 R P > 6. Asp_N 0 D - > 7. CNBr 1 M - > 8. Glu_C 1 DE P > 9. PepsinA 1 FL P > 10. Chymotrypsin 1 FWYL P > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/0760d2ad-3805-4d08-a27c-3af1c902400bn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/0760d2ad-3805-4d08-a27c-3af1c902400bn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. 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