XTandem and k-score

[Rishika Bisaria]

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.

[Jimmy Eng]

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>

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[Rishika Bisaria]

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 

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[Jimmy Eng]

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/ 

[Rishika Bisaria]

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

[Joseph Slagel]

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

[Rishika Bisaria]

Thank you.Will do it.

Regards,

Rishika

[Rishika Bisaria]

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