|   | mwcontam | 
The output of mwcontam, with minimal editing, can be added to the data file for the mwfilter program ('Emwfilter.dat').
| % mwcontam Shows molwts that match across a set of files Molecular weights file list: ../data/mw2.dat,mw3.dat Ppm tolerance [50.0]: Molecular weights output file [outfile.mwcontam]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-files]             filelist   Molecular weights file list
   -tolerance          float      [50.0] Ppm tolerance (Any numeric value)
  [-outfile]           outfile    [*.mwcontam] Molecular weights output file
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-files] (Parameter 1) | Molecular weights file list | Comma-separated file list | comma-separated file list | 
| -tolerance | Ppm tolerance | Any numeric value | 50.0 | 
| [-outfile] (Parameter 2) | Molecular weights output file | Output file | <*>.mwcontam | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| 20.0 33.0 67.0 128.0 415.0 999.0 | 
| 13.0 41.0 67.0 415.0 846.0 781.0 | 
| 3.0 18.0 67.0 124.0 197.0 236.0 415.0 587.0 632.0 | 
The input is a comma-separated list of files containing simple list of experimental molecular weights.
There should be one weight per line.
Comments in the data file start with a '#' character in the first column.
Blank lines are ignored.
| 67.000 415.000 | 
The output of mwcontam, with minimal editing, can be added to the data file for the mwfilter program ('Emwfilter.dat'). For example you might like to fetch 'Emwfilter.dat' using embossdata (as described in the mwfilter documentation) and edit it to include the lines:
# data produced from the program mwcontam mwcontam 67.000 mwcontam 415.000
| Program name | Description | 
|---|---|
| backtranambig | Back translate a protein sequence to ambiguous codons | 
| backtranseq | Back translate a protein sequence | 
| charge | Protein charge plot | 
| checktrans | Reports STOP codons and ORF statistics of a protein | 
| compseq | Count composition of dimer/trimer/etc words in a sequence | 
| emowse | Protein identification by mass spectrometry | 
| freak | Residue/base frequency table or plot | 
| iep | Calculates the isoelectric point of a protein | 
| mwfilter | Filter noisy molwts from mass spec output | 
| octanol | Displays protein hydropathy | 
| pepinfo | Plots simple amino acid properties in parallel | 
| pepstats | Protein statistics | 
| pepwindow | Displays protein hydropathy | 
| pepwindowall | Displays protein hydropathy of a set of sequences |