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mwcontam |
Function
Shows molwts that match across a set of filesDescription
mwcontam finds molecular weights that are common between a set of mass spectrometry result files. 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 output of mwcontam, with minimal editing, can be added to the data file for the mwfilter program ('Emwfilter.dat').
Usage
Here is a sample session with mwcontam
% mwcontam Shows molwts that match across a set of files Comma separated file list: ../data/mw2.dat,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
Command line arguments
Standard (Mandatory) qualifiers:
[-files] filelist Comma separated file list
-tolerance float Ppm tolerance
[-outfile] outfile Output file name
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 deaths
|
| Standard (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 |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Input file format
Input files for usage example
File: mw1.dat
20.0 33.0 67.0 128.0 415.0 999.0 |
File: mw2.dat
13.0 41.0 67.0 415.0 846.0 781.0 |
File: mw3.dat
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.
Output file format
The output is a list of the molecular weights common to all files.Output files for usage example
File: outfile.mwcontam
67.000 415.000 |
Data files
mwcontam uses no data files.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
Notes
None.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| 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 |
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK