Hi, e.g. I used X!Tandem in the past when searching for point mutations in proteins. For most tasks, I would use Comet, because it is easy to set-up and extremely fast.
Excerpts from [email protected]'s message of 2020-10-01 22:46:58 -0700: > Hello Robert, > > Thanks for replying. Can you please clarify what you mean by special > features of X!Tandem? I was using it hoping that I will be able to identify > more proteins in my sample after combing the search from Comet and > X!Tandem . Am I correct? > > On Wednesday, 30 September 2020 at 20:40:07 UTC+5:30 Robert wrote: > > > Hi, congratulations for using TPP! > > > > From my experience, comet is much more performant, I only would use > > X!Tandem if you need special features of it. > > > > Best, Robert > > > > Excerpts from [email protected]'s message of 2020-09-29 22:43:24 -0700: > > > Hello, > > > > > > I am a novice using TPP v5.2.0 Flammagenitus on a workstation (Intel, > > > Xeon, E5-2630 ver.5, 32Gb RAM, win 10). I have successfully run Comet, > > > however, the X!Tandem search is still on , its been more than 56 hours. > > How > > > much time does it take to complete the search? > > > What is the issue with the search? Please help. > > > > > > > > > *The params file is: * > > > *<?xml version="1.0" encoding="UTF-8"?>* > > > > > > *-<bioml>* > > > > > > *<note label="list path, default parameters" > > > type="input">D:/TPP/data/params/isb_default_input_kscore.xml</note>* > > > > > > *<note label="spectrum, path" type="input">full_mzXML_filepath</note>* > > > > > > *<note label="output, path" type="input">full_tandem_output_path</note>* > > > > > > *<note label="output, log path" type="input"/>* > > > > > > *<note label="output, sequence path" type="input"/>* > > > > > > *<note label="list path, taxonomy information" > > > type="input">D:/TPP/data/params/taxonomy.xml</note>* > > > > > > *<note label="protein, taxon" type="input">protein_database</note>* > > > > > > *<note label="spectrum, parent monoisotopic mass error minus" > > > type="input">2.0</note>* > > > > > > *<note label="spectrum, parent monoisotopic mass error plus" > > > type="input">4.0</note>* > > > > > > *<note label="spectrum, parent monoisotopic mass error units" > > > type="input">Daltons</note>* > > > > > > *<note label="spectrum, parent monoisotopic mass isotope error" > > > type="input">no</note>* > > > > > > *<note label="residue, modification mass" > > type="input">57.021464@C</note>* > > > > > > *<note label="residue, potential modification mass" > > > type="input">15.994915@M</note>* > > > > > > *<note label="residue, potential modification motif" type="input"/>* > > > > > > *<note label="protein, N-terminal residue modification mass" > > type="input"/>* > > > > > > *<note label="protein, C-terminal residue modification mass" > > type="input"/>* > > > > > > *<note label="protein, cleavage semi" type="input">yes</note>* > > > > > > *<note label="scoring, maximum missed cleavage sites" > > type="input">2</note>* > > > > > > *<note label="refine" type="input">no</note>* > > > > > > *<note label="refine, maximum valid expectation value" > > > type="input">0.1</note>* > > > > > > *<note label="refine, modification mass" type="input">57.012@C</note>* > > > > > > *<note label="refine, potential modification mass" > > > type="input">15.994915@M</note>* > > > > > > *<note label="refine, potential modification motif" type="input"/>* > > > > > > *<note label="refine, cleavage semi" type="input">yes</note>* > > > > > > *<note label="refine, unanticipated cleavage" type="input">no</note>* > > > > > > *<note label="refine, potential N-terminus modifications" type="input"/>* > > > > > > *<note label="refine, potential C-terminus modifications" type="input"/>* > > > > > > *<note label="refine, point mutations" type="input">no</note>* > > > > > > *<note label="refine, use potential modifications for full refinement" > > > type="input">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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/1601904675-sup-5819%40rob-Lenovo-Y720-15IKB.
