Are the tandem parameters ok? On Monday, 28 September 2020 at 16:16:39 UTC+5:30 [email protected] wrote:
> It has made 48 .PARAMS files and 1 .TANDEM file. > > tandem_params.xml is intact. > > > On Monday, 28 September 2020 at 15:41:49 UTC+5:30 [email protected] > wrote: > >> 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 command 1 out of 48. Its been more >> than 56 hours. How much time does it take to complete the search? I am >> working on 48.Raw files from a Thermo QExactive. The size of each file is >> approx. 500Mb. >> >> Fixed Mod: Carbamidomethyl on cysteine, Var mod : Oxidation of >> methionine and N-terminal acetylation. >> >> What is the issue with the search? >> >> >> *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/2a78e7f0-a053-4397-b976-38f503a84bebn%40googlegroups.com.
