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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 Comma-separated file list: ../../data/mw1.dat,../../data/mw2.dat,../../data/mw3.dat ppm tolerance [50.0]: Output file [outfile.mwcontam]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers: [-files] filelist Comma separated file list -tolerance float ppm tolerance [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) Associated qualifiers: "-outfile" related 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 required and optional values -debug boolean Write debug output to program.dbg -acdlog boolean Write ACD processing log to program.acdlog -acdpretty boolean Rewrite ACD file as program.acdpretty -acdtable boolean Write HTML table of options -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 deaths |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-files] (Parameter 1) |
Comma separated file list | Comma-separated file list | comma-separated file list |
-tolerance | ppm tolerance | Any numeric value | 50.0 |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.mwcontam |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced 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 |
---|---|
backtranseq | Back translate a protein sequence |
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein |
compseq | Counts the 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 |