mwcontam

 

Function

Shows molwts that match across a set of files

Description

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/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

Command line arguments

   Mandatory qualifiers:
  [-files]             filelist   Comma separated file list
   -tolerance          float      ppm tolerance
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


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)

Input file format

Input files for usage example

File: ../../data/mw1.dat

20.0
33.0
67.0
128.0
415.0
999.0

File: ../../data/mw2.dat

13.0
41.0
67.0
415.0
846.0
781.0

File: ../../data/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 nameDescription
backtranseqBack translate a protein sequence
chargeProtein charge plot
checktransReports STOP codons and ORF statistics of a protein
compseqCounts the composition of dimer/trimer/etc words in a sequence
emowseProtein identification by mass spectrometry
freakResidue/base frequency table or plot
iepCalculates the isoelectric point of a protein
mwfilterFilter noisy molwts from mass spec output
octanolDisplays protein hydropathy
pepinfoPlots simple amino acid properties in parallel
pepstatsProtein statistics
pepwindowDisplays protein hydropathy
pepwindowallDisplays protein hydropathy of a set of sequences

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Written (July 2002) - Alan Bleasby.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments