Data file format converter, from DTASelect-filter.txt files (output from DTASelect software) to mzIdentML version 1.1.0 and 1.2.0
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README.md

DTASelect2MzId

Data file format converter, from DTASelect-filter.txt files (output from DTASelect software) to mzIdentML version 1.1.0 and 1.2.0

Download: Latest version available at: [http://sealion.scripps.edu/dtaselect2mzid/]

Usage:

DTASelect2MzId -i [input file or folder]  
 
 -d,--decoy <arg>                 [OPTIONAL] decoy regular expression. Ignores matching entries. Example: 'Reverse'.
   
 -i,--input <arg>                 path to the input file (or folder)   
   
 -n,--file_name <arg>             [OPTIONAL] To use a input file name different from the default 'DTASelect-filter.txt'  
    
 -ns,--no_spectra                 [OPTIONAL] If provided, no MS2 files will be readed in order to match PSMs with spectra in the output file  
                                  
 -r,--recursive                   [OPTIONAL] In case of using a folder as input '-i', it will search recursively for all the DTASelect-filter.txt files.
 
 -rs,--referenceToSpectra <arg>   [OPTIONAL] Reference to spectra. Possible values: 'MZXML', 'MS2'. Default: 'MS2'  
 
 -sky,--skyline <arg>             [OPTIONAL] Whether the generated mzIdentML will be compatible with skyline for importing results. If  
                                  'true', the file will contain additional features to make it compatible. Possible values: 'true' or 'false'. Default: 'true'  
                                  
 -u,--unique_output_file          [OPTIONAL] A single mzIdentML file will be created collapsing all the information of all the input files. Otherwise, a mzIdentML file will be created for each input file.  
   
 -v,--version <arg>               [OPTIONAL] Version of the output mzIdentML '-v', Possible values: '1.1.1', '1.2.0'. Default: 1.1.1  

Note about referenceToSpectra parameter:

  • The use of the parameter referenceToSpectra will make the converter to read the associated spectra files (mzXML or ms2) in order to properly include the reference to the spectra of the peptide spectrum matches.
  • However, the converter will not include the actual identified/matched fragment ions in the output mzIdentML file.
  • As an example, if the converter reads the spectrum line from the DTASelect file as:
*	042117_PB1_trypsin.18815.18815.3	1.7635	0.3047	100.0	2275.1868	2275.1765	4.5	1986159.2	2	3.9090989	12.0	31.5	1	G.GGWSGSHAFILVM(15.9949)AALTTRAGR.K 

it will look for the file named as

042117_PB1_trypsin.extension

where 'extension' is the parameter value of -rs input parameter.

  • If everything goes well, then you will be able to open the output mzIdentML in a software sich as PRIDE Inspector and then be able to select the associated spectra files, which will load the matches spectra in the screen with their corresponding annotated matched fragment ions.

How to integrate search engine input parameters in the mzIdentML?

You should have a search.xml file in the same forlder as the input files. If it is found, elements such as:

  • Enzymes,
  • FragmentTolerance,
  • ParentTolerance,
  • SearchType or
  • ModificationParams

will be added to the SpectrumIdentificationProtocol element of the resulting mzIdentML file.


Contact Salvador Martinez-Bartolome at salvador at scripps.edu for more help