| 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: ../../data/molwts.dat
    ppm tolerance [50.0]:
    Output file [molwts.mwfilter]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

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

       Optional qualifiers:
       -showdel            boolean    Output deleted mwts

       Advanced qualifiers:
       -datafile           string     Data file of noisy molecular weights

       Associated qualifiers:
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | Molecular weight file input | Input file | Required
-tolerance | ppm tolerance | Any numeric value | 50.0
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.mwfilter
Optional qualifiers | Allowed values | Default
-showdel | Output deleted mwts | Boolean value Yes/No | No
Advanced qualifiers | Allowed values | Default
-datafile | Data file of noisy molecular weights | Any string is accepted | Emwfilter.dat

## Input file format

### Input files for usage example

### File: ../../data/molwts.dat

    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

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.

## Output file format

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

### Output files for usage example

### File: molwts.mwfilter

    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
    1880.841178

## 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
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
mwcontam | Shows molwts that match across a set of files
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 (ableasby © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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