Documentation on how to modify a X!Tandem params file can be found here: http://www.thegpm.org/TANDEM/api/index.html
On Oct 21, 2:43 am, Fournier <[email protected]> wrote: > I would like to use X!Tandem with TPP to compare the results with > Sequest. > However, I can not create the file parameter X!Tandem. I would like > that the parameters are the same ones I use to Sequest: > > [SEQUEST] > first_database_name = C:\Xcalibur\database\base_reduite.fasta > second_database_name = > peptide_mass_tolerance = 10.00000 > peptide_mass_units = 2 ; 0=amu, 1=mmu, 2=ppm > ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 > fragment_ion_tolerance = 0.50000 ; for trap data leave at > 1.0, for accurate mass data use values < 1.0 > fragment_ion_units = 0 ; 0=amu, 1=mmu > num_output_lines = 20 ; # peptide results to show > num_results = 250 ; # results to store > num_description_lines = 3 ; # full protein descriptions to > show for top N peptides > show_fragment_ions = 0 ; 0=no, 1=yes > print_duplicate_references = 0 ; number of duplicate references > reported > enzyme_info = No_Enzyme 0 0 - - > max_num_differential_per_peptide = 3 ; max # of diff. mod in > a peptide > diff_search_options = 0.000000 S 0.000000 C 0.000000 M 0.000000 X > 0.000000 T 0.000000 Y > term_diff_search_options = 0.000000 0.000000 > nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward > three, 8-reverse three, 9=all six > mass_type_parent = 1 ; 0=average masses, 1=monoisotopic > masses > mass_type_fragment = 1 ; 0=average masses, 1=monoisotopic > masses > normalize_xcorr = 0 ; use normalized xcorr values in > the out file > remove_precursor_peak = 0 ; 0=no, 1=yes > ion_cutoff_percentage = 0.00000 ; prelim. score cutoff % as > a decimal number i.e. 0.30 for 30% > max_num_internal_cleavage_sites = 2 ; maximum value is 12 > protein_mass_filter = 0 0 ; enter protein mass min & max > value ( 0 for both = unused) > match_peak_count = 0 ; number of auto-detected peaks to > try matching (max 5) > match_peak_allowed_error = 1 ; number of allowed errors in > matching auto-detected peaks > match_peak_tolerance = 1.00000 ; mass tolerance for > matching auto-detected peaks > partial_sequence = > sequence_header_filter = > digest_mass_range = 200.0 4000.0 > > add_Cterm_peptide = 0.00000 ; added to each peptide C- > terminus > add_Cterm_protein = 0.00000 ; added to each protein C- > terminus > add_Nterm_peptide = 0.00000 ; added to each peptide N- > terminus > add_Nterm_protein = 0.00000 ; added to each protein N- > terminus > add_G_Glycine = 0.00000 ; added to G > add_A_Alanine = 0.00000 ; added to A > add_S_Serine = 0.00000 ; added to S > add_P_Proline = 0.00000 ; added to P > add_V_Valine = 0.00000 ; added to V > add_T_Threonine = 0.00000 ; added to T > add_C_Cysteine = 0.00000 ; added to C > add_L_Leucine = 0.00000 ; added to L > add_I_Isoleucine = 0.00000 ; added to I > add_X_LorI = 0.00000 ; added to X > add_N_Asparagine = 0.00000 ; added to N > add_O_Ornithine = 0.00000 ; added to O > add_B_avg_NandD = 0.00000 ; added to B > add_D_Aspartic_Acid = 0.00000 ; added to D > add_Q_Glutamine = 0.00000 ; added to Q > add_K_Lysine = 0.00000 ; added to K > add_Z_avg_QandE = 0.00000 ; added to Z > add_E_Glutamic_Acid = 0.00000 ; added to E > add_M_Methionine = 0.00000 ; added to M > add_H_Histidine = 0.00000 ; added to H > add_F_Phenylalanine = 0.00000 ; added to F > add_R_Arginine = 0.00000 ; added to R > add_Y_Tyrosine = 0.00000 ; added to Y > add_W_Tryptophan = 0.00000 ; added to W > add_J_user_amino_acid = 0.00000 ; value for J > add_U_user_amino_acid = 0.00000 ; value for U > > Could you help me? > For instance, I have for X!Tandem Parameter: > > <?xml version="1.0" encoding="UTF-8" ?> > - <bioml> > <note>DEFAULT PARAMETERS. The value of > "isb_default_input_kscore.xml" is recommended. Change to > "isb_default_input_native.xml" for native X!Tandem scoring.</note> > <note type="input" label="list path, default parameters">c:/Inetpub/ > wwwroot/ISB/data/parameters/isb_default_input_kscore.xml</note> > <note>FILE LOCATIONS. Replace them with your input (.mzXML) file and > output file -- these are REQUIRED. Optionally a log file and a > sequence output file of all protein sequences identified in the first- > pass can be specified. Use of FULL path (not relative) paths is > recommended.</note> > <note type="input" label="output, log path" /> > <note type="input" label="output, sequence path" /> > <note>TAXONOMY FILE. This is a file containing references to the > sequence databases. Point it to your own taxonomy.xml if needed.</ > note> > <note>PROTEIN SEQUENCE DATABASE. This refers to identifiers in the > taxomony.xml, not the .fasta files themselves! Make sure the database > you want is present as an entry in the taxonomy.xml referenced above. > This is REQUIRED.</note> > <note>PRECURSOR MASS TOLERANCES. In the example below, a -2.0 Da to > 4.0 Da (monoisotopic mass) window is searched for peptide candidates. > Since this is monoisotopic mass, so for non-accurate-mass instruments, > for which the precursor is often taken nearer to the isotopically > averaged mass, an asymmetric tolerance (-2.0 Da to 4.0 Da) is > preferable. This somewhat imitates a (-3.0 Da to 3.0 Da) window for > averaged mass (but not exactly)</note> > <note type="input" label="spectrum, parent monoisotopic mass error > minus">2.0</note> > <note type="input" label="spectrum, parent monoisotopic mass error > plus">4.0</note> > <note type="input" label="spectrum, parent monoisotopic mass error > units">Daltons</note> > <note>The value for this parameter may be 'Daltons' or 'ppm': all > other values are ignored</note> > <note type="input" label="spectrum, parent monoisotopic mass isotope > error">no</note> > <note>This allows peptide candidates in windows around -1 Da and -2 > Da from the acquired mass to be considered. Only applicable when the > minus/plus window above is set to less than 0.5 Da. Good for accurate- > mass instruments for which the reported precursor mass is not > corrected to the monoisotopic mass.</note> > <note>MODIFICATIONS. In the example below, there is a static > (carbamidomethyl) modification on C, and variable modifications on M > (oxidation). Multiple modifications can be separated by commas, as in > "8...@s,8...@t". Peptide terminal modifications can be specified with > the symbol '[' for N-terminus and ']' for C-terminus, such as > 4...@[ .</note> > <note type="input" label="residue, modification mass">442.2...@c</ > note> > <note type="input" label="residue, potential modification > mass">8...@c,1...@m</note> > <note type="input" label="residue, potential modification motif" /> > <note>You can specify a variable modification only when present in a > motif. For instance, 0....@n!{p}[st] is a deamidation modification on > N only if it is present in an N[any but P][S or T] motif (N- > glycosite).</note> > <note type="input" label="protein, N-terminal residue modification > mass" /> > <note type="input" label="protein, C-terminal residue modification > mass" /> > <note>These are *static* modifications on the PROTEINS' N or C- > termini.</note> > <note>SEMI-TRYPTICS AND MISSED CLEAVAGES. In the example below, > semitryptic peptides are allowed, and up to 2 missed cleavages are > allowed.</note> > <note type="input" label="protein, cleavage semi">yes</note> > <note type="input" label="scoring, maximum missed cleavage sites">2</ > note> > <note>REFINEMENT. Do not use unless you know what you are doing. Set > "refine" to "yes" and specify what you want to search in the > refinement. For non-confusing results, repeat the same modifications > you set above for the first-pass here.</note> > <note type="input" label="refine">yes</note> > <note type="input" label="refine, maximum valid expectation > value">0.1</note> > <note type="input" label="refine, modification mass">442.2...@c</ > note> > <note type="input" label="refine, potential modification mass">8...@c, > 1...@m</note> > <note type="input" label="refine, potential modification motif" /> > <note type="input" label="refine, cleavage semi">yes</note> > <note type="input" label="refine, unanticipated cleavage">no</note> > <note type="input" label="refine, potential N-terminus > modifications" /> > <note type="input" label="refine, potential C-terminus > modifications" /> > <note type="input" label="refine, point mutations">no</note> > <note type="input" label="refine, use potential modifications for > full refinement">no</note> > </bioml> > > What should I change? > Thank you for your future answer! -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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