Thank you.Will look into the parameters again. Regards, Rishika
On Tue, Aug 13, 2013 at 4:35 PM, David Shteynberg < [email protected]> wrote: > Usually when the search returns no good results (which is what TPP is > telling you here) it is one of three possible options: > > 1. Bad data quality > 2. Wrong search parameters (incorrect static mass mod or wrong enzyme > info. etc) > 3. Wrong database (incorrect organism etc) > > Please consider these possibilities in your search results. > > -David > > > On Tue, Aug 13, 2013 at 12:00 PM, Rishika Bisaria <[email protected] > > wrote: > >> I am sorry but I am really very new to Proteomics and I am not able to >> figure out the reason for error. >> >> >> >> >> On Tue, Aug 13, 2013 at 2:56 PM, David Shteynberg < >> [email protected]> wrote: >> >>> Any reason you would see this other than Tandem search failed to >>> generate results? >>> >>> Parsing search results "SP062512_062912_IP0201_AX01_23to24 (X! Tandem >>> (k-score))"... >>> => Total of 0 hits. >>> => Total of 0 decoy hits. >>> => Total of 0 excluded hits. >>> >>> >>> On Tue, Aug 13, 2013 at 11:41 AM, Rishika Bisaria < >>> [email protected]> wrote: >>> >>>> Hi, >>>> Thank you for the reply. >>>> Actually I want to follow this pipeline: >>>> >>>> Tandem->peptideprophet->q3new->proteinprophet->Q3proteinRatioParser. >>>> >>>> And also when I am using Xinteract , I am getting the below error: >>>> >>>> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i >>>> interact.iproph.pep.xml" >>>> Analyzing interact.iproph.pep.xml ... >>>> Reading NSS model ... >>>> Reading NRS model ... >>>> Reading NSE model ... >>>> Reading NSI model ... >>>> Reading NSM model ... >>>> Reading NSP model ... >>>> Parsing search results "SP062512_062912_IP0201_AX01_23to24 (X! Tandem >>>> (k-score))"... >>>> => Total of 0 hits. >>>> => Total of 0 decoy hits. >>>> => Total of 0 excluded hits. >>>> command completed in 1 sec >>>> >>>> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/xtandem/interact.iproph.pep.xml" >>>> >>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/xtandem/interact.iproph.pep.xml" failed: Unknown error >>>> >>>> command "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I >>>> c:/xtandem/interact.iproph.pep.xml" exited with non-zero exit code: >>>> -1073741819 >>>> QUIT - the job is incomplete >>>> >>>> >>>> >>>> >>>> >>>> On Tue, Aug 13, 2013 at 2:28 PM, David Shteynberg < >>>> [email protected]> wrote: >>>> >>>>> You pipeline is missing the InteractParser step. Once you have a >>>>> pep.xml file from Tandem you can run "xinteract -ip -p0 "on it to generate >>>>> InteractParser->PeptideProphet->iProphet->ProteinProphet pipeline results. >>>>> >>>>> -David >>>>> >>>>> >>>>> On Tue, Aug 13, 2013 at 10:16 AM, Rishika Bisaria < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi, >>>>>> I am able to run successfully the TPP pipeline on one of the mzXML >>>>>> file.But on using TPP on other mzXML file , ProteinProphet is throwing >>>>>> error stating that did you forgot to run PeptideProphet. >>>>>> I have crossed checked all the parameters , they are correct.I am >>>>>> using the latest version of TPP on windows and running it using >>>>>> commandline. >>>>>> >>>>>> 1.tandem input.xml >>>>>> 2.Tandem2XML output.2013_07_24_13_24_28.t.xml >>>>>> output.2013_07_24_13_24_28.pep.xml >>>>>> 3.PeptideProphetParser output.2013_07_24_13_24_28.pep.xml MINPROB=0.2 >>>>>> 4.ProteinProphet output.2013_07_24_13_24_28.pep.xml >>>>>> c:\Inetpub\wwwroot\out1.prot.xml >>>>>> >>>>>> **** >>>>>> >>>>>> P.S. Everytime I am changing the parameters in input.xml file.I am >>>>>> using k-score function. >>>>>> >>>>>> >>>>>> Thanks, >>>>>> Rishika >>>>>> >>>>>> -- >>>>>> 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 http://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "spctools-discuss" group. >>>>> To unsubscribe from this topic, visit >>>>> https://groups.google.com/d/topic/spctools-discuss/W_HCVBI82aM/unsubscribe >>>>> . >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> [email protected]. >>>>> >>>>> To post to this group, send email to [email protected] >>>>> . >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/groups/opt_out. >>>>> >>>> >>>> -- >>>> 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 http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>>> >>>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "spctools-discuss" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/spctools-discuss/W_HCVBI82aM/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, send an email to >>> [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> 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 http://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/W_HCVBI82aM/unsubscribe > . > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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