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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
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| 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.