If you get LabKey Server (free download, see www.labkey.com, or try it online) the default scoring engine is XTandem. In your case just select No Enzyme and point it to the fasta file and run the search. I don't see any non-standard options or modifications specified in your sequest.params, so there doesn't seem to be a lot to translate. Labkey Serever writes out a default.xml and a run-specific tandem.xml with overrides. Combined the two make up the tandem parameters file.
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. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
