Howto - Census Label free analysis - May 4, 2009 updated

• Requirements and limitations
  • Census version 1.55 or higher is required to run label free analysis. The latest version can be downloaded at Yates web site
  • JDK 1.6 or higer is required. Download it at Java home page
  • GUI version for label free is not supported yet. You need to run it at command lines
  • Currently label free analsysis requires DTASelect output files and MS1 files. It does not support pepXML or mzXML for label free analysis. MS1 files can be generated by RawXtractor, and the RawXtractor can be downloaded at Yates web site

• Prepare Census config file
  • Sample config file can be download at sample file link. You can directly modify it by using any editor software.
  • mass_accuracy : ppm unit should be adjusted based on your mass spectrometry instrument
  • max_win : # of scans the Census searches for peak finding on each side of peak
  • changing avg_interval, peak_margin, area_threshold tags is not recommended
  • database_file: path and file name of fasta database
  • sample : user defined sample or experiment name
  • file : path and extension of ms1 file. By using wild card, Census loads multiple files. Census expects that the path contains DTASelect-filter.txt file.
  • element_comp : element compostion of each residue
  • *, #, @ signs indicate modification

• Run Census
  • java -Xmx1500M -jar census.jar -c census_config_label_free_area.xml. Please change the memory size "1500M" to different value depending on your computer to run on.

• Output file
  • "census_label_free_result_with_id.txt" is the final result file.