Parameter file for X!Tandem

[Fournier]

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
"80.0@S,80.0@T". Peptide terminal modifications can be specified with
the symbol '[' for N-terminus and ']' for C-terminus, such as
42.0@[ .</note>
<note type="input" label="residue, modification mass">442.2000@C</
note>
<note type="input" label="residue, potential modification
mass">8.0@C,16.0@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, 0.998@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">442.2000@C</
note>
<note type="input" label="refine, potential modification mass">8.0@C,
16.0@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!

[Kristian]

Documentation on how to modify a X!Tandem params file can be found
here: http://www.thegpm.org/TANDEM/api/index.html

[PeterAtLabKey]

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 <beb...@msn.com> wrote: