Hello,
Is it possible that you are running a version of X!Tandem that is different from the one included with the TPP? X!Tandem that is included with the TPP supports the k-score plugin, I just tested in TPP5.1.0 by running a search using Petunia interface to the TPP. You can find out what tandem version is being called by typing "*where tandem.exe"* into a Windows Command Prompt. The TPP version of tandem.exe is installed in *C:/TPP/bin/tandem.exe *by default. You will have to call tandem.exe with the full path when you run the search on the commandline. -David On Wed, Dec 27, 2017 at 5:04 AM, md qudratullah <[email protected]> wrote: > 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> >> >> >> -- > 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 [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
