Hardklör 1.0

Config File Overview

Hardklör configuration files are in ASCII text format and can be used to set parameters and operate Hardklör in batch mode. There are two basic format structures: parameter lines and action lines. Parameter lines allow parameters to be set on a global level, i.e. you can set the parameter once and it will be applied to every data file being analyzed in your batch. Parameters are entered as one parameter per line and begin with a dash (-). Action lines execute analysis on a data file. Only one data file is specified per action line, however, a config file may contain a batch of several action lines. Action lines always specify a data file and an output file: <MS1 file> <output file> Additionally, action lines may contain parameters that will only be applied to the analysis of the data file on that line. Finally, the # sign at the beginning of a line indicates a comment, and the line will be skipped during execution. Below are some examples of configuration files.

Example Config File #1


      # Set paths to DAT files

     -mdat \usr\local\hardklor\ISOTOPE.DAT

     -hdat \usr\local\hardklor\Hardklor.dat



      # Set global parameters

      -d 2

      -sn 2.5

      -corr 0.95

      -chMax 5

      -res 200000 FTICR

      -a FastFewestPeptides

      -cdm Q



      # Files to analyze

      File1.ms1 File1output.txt

      File2.ms1 File2output.txt

      File3.ms1 File3output.txt



      # Analyze File1.ms1 again with a different 

      # charge determination method

      File1.ms1 File1outputB.txt -cdm C

In this example, a batch analysis is being performed. There are a total of four analyses for three data files. Note the first two flags set indicate the locations of the Mercury and Hardklör data files. Setting these paths at the top of the config file allows the analysis to take place in the working directory instead of the directory where Hardklör is installed. Eight global parameters are set at the top of the config file. These parameters are set globally, and thus they are applied to all four analyses. Any parameters not specified use the default values. Below the parameters are three action lines specifying the input and output file names. The last line shows a second analysis being performed on the first data file. Notice that this line has a parameter specifying a different charge determination method than the previous analyses. This parameter value in the action line overrides the global parameter value.

Example Config File #2


      # Set global parameters

      -sn 2

      -corr 0.85

      -res 200000 FTICR

      -a FastFewestPeptides

      -cdm Q


      # Files to analyze

      File1.ms1 File1output.txt

      File2.ms1 File2output.txt

      File3.ms1 File3output.txt



      # Change some global parameters

      -sn 3

      -corr 0.95

      -d 2



      # Analyze the next three files with the

	# new global parameters

      File4.ms1 File4output.txt

      File5.ms1 File5output.txt

      File6.ms1 File6output.txt

In example #2, global parameters are set at the top of the config file and analysis is performed on three data files. Then, about halfway down, three of the global parameters are set to new values. The last three files being analyzed will still have -res 200000 FTICR, -a FastFewestPeptides, and -cdm Q as parameter settings, but their signal-over-noise threshold was changed to 3, and the correlation score changed to 0.95. In addition to these changes, the -d 2 parameter was added to their analysis.

Example Config File #3


      # Set global parameters

      -sn 1

      -corr 0.95

      -res 50000 FTICR

      -a FastFewestPeptides

      -cdm Q


      # Files to analyze

      File1.ms1 File1output.txt -m 0.50H1

      File2.ms1 File2output.txt -m 0.75H1

      File3.ms1 File3output.txt -m 0.90H1

Example #3 is very similar to the previous examples, but the most distinguishing feature is that it emphasizes use of Hardklör's ability to differentiate peptides that are isotopically enriched from those that have the natural abundance of isotopes. Each file was presumably from a sample with a different enrichment level than the other samples. The first file is analyzed with 50% deuterium enrichment, the second file with 75% deuterium enrichment, and the third file with 90% deuterium enrichment.

Config File Overview

Example Config File #1

Example Config File #2

Example Config File #3

Hardklör is Copyright ©2007 University of Washington. All rights reserved. Written by Michael R. Hoopmann, Michael J. MacCoss, in the Department of Genome Sciences at the University of Washington.