EMBOSS: mwfilter

| ## EMBOSS: mwfilter

# Program mwfilter

## Function

Filter noisy molwts from mass spec output

## Description

mwfilter is designed to remove unwanted (noisy) data from mass spectrometry output in proteomics. Given a list of molecular weights this program removes those which are:

- Contaminating trypsin or keratin
- Modified oxy-methionine or oxy-threonine
- Peaks associated with sodium ions.

The last two operations can be done as most peaks are reported in both modified and unmodified forms. Removal of modified peaks aids in database searching for protein identification.

## Usage

Here is a sample session with mwfilter:

    % mwfilter
    Filter noisy molwts from mass spec output
    Input file: molwts.dat
    ppm tolerance [50.0]:
    Output file [molwts.mwfilter]:

## Command line arguments

       Mandatory qualifiers:
      [-infile]            infile     Molecular weight file input
       -tolerance          float      ppm tolerance
      [-outfile]           outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -datafile           string     Data file of noisy molecular weights

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | Molecular weight file input | Input file | Required
-tolerance | ppm tolerance | Any integer value | 50.0
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.mwfilter
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-datafile | Data file of noisy molecular weights | Any string is accepted | Emwfilter.dat

## Input file format

The input file is a simple list of the 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.

An example of the input data follows:

    874.364756
    927.450380
    1045.572
    1068.397129
    1121.431124
    1163.584593
    1305.660840
    1428.596448
    1479.748341
    1502.549157
    1554.591658
    1567.686209
    1576.708354
    1639.868056
    1748.611920
    1753.745298
    1880.841178
    2383.99

## Output file format

The output is a list of the molecular weights with the unwanted (noisy) data removed.

An example of the output data follows:

    874.364756
    927.450380
    1068.397129
    1121.431124
    1163.584593
    1305.660840
    1428.596448
    1479.748341
    1502.549157
    1554.591658
    1567.686209
    1576.708354
    1639.868056
    1748.611920
    1753.745298

## Data files

The program reads the data file Emwfilter.dat for the molecular weights of items to be deleted from the experimental data.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## 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 sequence
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
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)

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

## History

Written (Jan 2002) - Alan Bleasby.

## Target users

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

## Comments