Hi, I have got the results of XTandem, Tandem2XML, PeptideProphetParser . But on running the Protein Prophet it is showing did not find any PeptideProphet results in input data! Did you forget to run PeptideProphet? Please guide me where I am going wrong. It is not throwing any error when I am running PeptideProphet.
Regards, Rishika On Fri, Jul 26, 2013 at 2:05 PM, Rishika Bisaria <[email protected]>wrote: > Thank you.Will do it. > > Regards, > Rishika > > > On Fri, Jul 26, 2013 at 2:03 PM, Joseph Slagel < > [email protected]> wrote: > >> Rishika, >> >> The TPP version of X!Tandem has some dependencies (such as mzParser) that >> are outside of the src_tpp directory. >> >> I hate to say it but the easiest thing to do is download and build all of >> TPP. >> >> -Joe >> >> >> >> On Fri, Jul 26, 2013 at 9:44 AM, Rishika Bisaria <[email protected] >> > wrote: >> >>> Hi, >>> Thank you for the reply. >>> I copied all teh files to src folder , changed the permission0 and ran >>> the make command. >>> But still I am getting this error: >>> >>> >>> In file included from loadmzparser.cpp:7:0: >>> loadmzparser.h:47:2: error: ‘BasicSpectrum’ does not name a type >>> loadmzparser.h:48:2: error: ‘MzParser’ does not name a type >>> loadmzparser.cpp: In constructor >>> ‘loadmzparser::loadmzparser(std::vector<mspectrum>&, mspectrumcondition&, >>> mscore&)’: >>> loadmzparser.cpp:13:2: error: ‘mzp’ was not declared in this scope >>> loadmzparser.cpp:13:12: error: expected type-specifier before ‘MzParser’ >>> loadmzparser.cpp:13:12: error: expected ‘;’ before ‘MzParser’ >>> loadmzparser.cpp: In destructor ‘virtual loadmzparser::~loadmzparser()’: >>> loadmzparser.cpp:20:9: error: ‘mzp’ was not declared in this scope >>> loadmzparser.cpp: In member function ‘virtual bool loadmzparser::get()’: >>> loadmzparser.cpp:25:8: error: ‘mzp’ was not declared in this scope >>> loadmzparser.cpp:26:6: error: ‘s’ was not declared in this scope >>> loadmzparser.cpp:28:6: error: ‘s’ was not declared in this scope >>> loadmzparser.cpp: In member function ‘int loadmzparser::guessCharge()’: >>> loadmzparser.cpp:54:17: error: ‘s’ was not declared in this scope >>> loadmzparser.cpp: In member function ‘virtual bool >>> loadmzparser::open(std::string&)’: >>> loadmzparser.cpp:66:9: error: ‘mzp’ was not declared in this scope >>> loadmzparser.cpp: In member function ‘void >>> loadmzparser::processSpectrum(int)’: >>> loadmzparser.cpp:74:12: error: ‘s’ was not declared in this scope >>> loadmzparser.cpp:79:24: error: ‘CID’ was not declared in this scope >>> loadmzparser.cpp:80:29: error: ‘ETD’ was not declared in this scope >>> loadmzparser.cpp:80:55: error: ‘ETDSA’ was not declared in this scope >>> make: *** [loadmzparser.o] Error 1 >>> >>> Thank you. >>> >>> Regards , >>> Rishika >>> >>> >>> On Thu, Jul 25, 2013 at 8:09 PM, Jimmy Eng <[email protected]> wrote: >>> >>>> That's an old page you're referencing. Try these files: >>>> >>>> >>>> http://sourceforge.net/p/sashimi/code/6253/tree/tags/release_4-6-3/trans_proteomic_pipeline/extern/xtandem/src_tpp/ >>>> >>>> >>>> >>>> On Thu, Jul 25, 2013 at 4:46 PM, Rishika Bisaria < >>>> [email protected]> wrote: >>>> >>>>> Hi , >>>>> Thank you for the reply. >>>>> I downloaded the two files in src folder of XTandem from >>>>> https://proteomics.fhcrc.org/CPAS/Project/Published%20Experiments/Tandem%20Pluggable%20Scoring/begin.view >>>>> ?. >>>>> But I am getting error on running the make command. >>>>> >>>>> g++ -M -O2 -DGCC4_3 mscore_k.cpp > mscore_k.d >>>>> g++ -M -O2 -DGCC4_3 mscore_k.cpp | sed s/\\.o/.d/ > mscore_k.d >>>>> g++ -O2 -DGCC4_3 -c -o mscore_k.o mscore_k.cpp >>>>> mscore_k.cpp: In member function ‘virtual mplugin* >>>>> mscorefactory_k::create_plugin()’: >>>>> mscore_k.cpp:34:25: error: cannot allocate an object of abstract type >>>>> ‘mscore_k’ >>>>> mscore_k.h:84:7: note: because the following virtual functions are >>>>> pure within ‘mscore_k’: >>>>> mscore.h:382:21: note: virtual float mscore::ion_check(long >>>>> unsigned int, size_t) >>>>> mscore_k.cpp: At global scope: >>>>> mscore_k.cpp:365:7: error: ‘mscore_tandem’ has not been declared >>>>> mscore_k.cpp: In function ‘float ion_check(long unsigned int, size_t)’: >>>>> mscore_k.cpp:371:36: error: ‘m_vmiType’ was not declared in this scope >>>>> make: *** [mscore_k.o] Error 1 >>>>> >>>>> Thanks, >>>>> Rishika >>>>> >>>>> >>>>> >>>>> On Thu, Jul 25, 2013 at 4:44 PM, Jimmy Eng <[email protected]> wrote: >>>>> >>>>>> You would need a version of X!Tandem that has k-score in it so use >>>>>> the one distributed with the TPP. Beyond that, the minimum parameter to >>>>>> set would be: >>>>>> >>>>>> <note type="input" label="scoring, algorithm">k-score</note> >>>>>> >>>>>> >>>>>> On Thu, Jul 25, 2013 at 1:15 PM, Rishika Bisaria < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hi, >>>>>>> I am a newbie to proteomics analysis. >>>>>>> I wanted to know how can we use k-score in XTandem. Just modifying >>>>>>> the parameter in the file is sufficient or we have to make other changes >>>>>>> also. >>>>>>> Thank You. >>>>>>> >>>>>>> -- >>>>>>> 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/lpKfFoMiQS0/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/lpKfFoMiQS0/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/lpKfFoMiQS0/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.
