|   | mwcontam | 
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mwcontam finds molecular weights that are common between a set of mass spectrometry result files at a specified ppm tolerance. Such molecular weights are usually a form of contamination resulting from autolysis of a protease, degradation of the matrix or presence of keratin from the sample preparer. The input is a comma-separated list of files each containing a list of experimental molecular weights. The output is a file with a list of the molecular weights common to all files.
| % mwcontam Find weights common to multiple molecular weights 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
| 
Find weights common to multiple molecular weights files
Version: EMBOSS:6.6.0.0
   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-files] (Parameter 1) | filelist | Molecular weights file list | Comma-separated file list | comma-separated file list | 
| -tolerance | float | Ppm tolerance | Any numeric value | 50.0 | 
| [-outfile] (Parameter 2) | outfile | Molecular weights output file | Output file | <*>.mwcontam | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
| 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
The output of mwcontam, with minimal editing, can be added to the data file for the mwfilter program (Emwfilter.dat), which will then remove these weights from its input file of molecular weights. 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 nucleotide sequence | 
| backtranseq | Back-translate a protein sequence to a nucleotide sequence | 
| compseq | Calculate the composition of unique words in sequences | 
| emowse | Search protein sequences by digest fragment molecular weight | 
| freak | Generate residue/base frequency table or plot | 
| mwfilter | Filter noisy data from molecular weights file | 
| oddcomp | Identify proteins with specified sequence word composition | 
| pepdigest | Report on protein proteolytic enzyme or reagent cleavage sites | 
| pepinfo | Plot amino acid properties of a protein sequence in parallel | 
| pepstats | Calculate statistics of protein properties | 
| wordcount | Count and extract unique words in molecular sequence(s) | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.