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 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.
