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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
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. 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|
|Molecular weights file list||Comma-separated file list||comma-separated file list|
|-tolerance||Ppm tolerance||Any numeric value||50.0|
|Molecular weights output file||Output file||<*>.mwcontam|
|Additional (Optional) qualifiers||Allowed values||Default|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
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.
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
|backtranambig||Back-translate a protein sequence to ambiguous nucleotide sequence|
|backtranseq||Back-translate a protein sequence to a nucleotide sequence|
|charge||Draw a protein charge plot|
|checktrans||Reports STOP codons and ORF statistics of a protein|
|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|
|iep||Calculate the isoelectric point of proteins|
|mwfilter||Filter noisy data from molecular weights file|
|octanol||Draw a White-Wimley protein hydropathy plot|
|pepinfo||Plot amino acid properties of a protein sequence in parallel|
|pepstats||Calculates statistics of protein properties|
|pepwindow||Draw a hydropathy plot for a protein sequence|
|pepwindowall||Draw Kyte-Doolittle hydropathy plot for a protein alignment|
|wordcount||Count and extract unique words in DNA sequence(s)|