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:

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:

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 sequence
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
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 (Jan 2002) - Alan Bleasby.

Target users

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

Comments