>
> Hello.
> Whenever I run tandem (TPP5.1.0 ) through command line it shows the
> following the message on command line:
>
> "Loading spectraError: The plug-in 'scoring, algorithm, k-score' is not
> registered". I have been trying to run it for two days but all in vain.
> Please help me.
> My command is as follow: tandem tandem_params. Here is my tandem_params
> file..........
>
>
> <?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:\TPP\data\params\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="spectrum,
> path">C:\Users\Qudrat\Desktop\mass\MCF7_1</note>
> <note type="input" label="output,
> path">C:\Users\Qudrat\Desktop\mass\MCF7_1.tandem</note>
> <note type="input" label="output, log path"></note>
> <note type="input" label="output, sequence path"></note>
>
> <note> TAXONOMY FILE. This is a file containing references to the sequence
> databases. Point it to your own taxonomy.xml if needed.</note>
> <note type="input" label="list path, taxonomy
> information">C:\Users\Qudrat\Desktop\mass\taxonomy.xml</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 type="input" label="protein, taxon">mydatabase</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">57.021464@C</note>
> <note type="input" label="residue, potential modification
> mass">15.994915@M</note>
> <note type="input" label="residue, potential modification motif"></note>
> <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>
> <note type="input" label="protein, C-terminal residue modification
> mass"></note>
> <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">no</note>
> <note type="input" label="refine, maximum valid expectation
> value">0.1</note>
> <note type="input" label="refine, modification mass">57.012@C</note>
> <note type="input" label="refine, potential modification
> mass">15.994915@M</note>
> <note type="input" label="refine, potential modification motif"></note>
> <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>
> <note type="input" label="refine, potential C-terminus
> modifications"></note>
> <note type="input" label="refine, point mutations">no</note>
> <note type="input" label="refine, use potential modifications for full
> refinement">no</note>
>
>
>
>
> </bioml>
>
>
>
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