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EMBOSS: mwfilter
mwfilter

 

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Function

Filter noisy data from molecular weights file

Description

mwfilter removes unwanted (noisy) data from mass spectrometry output in proteomics. It reads an input file with a list of experimental molecular weights and writes the same data to an output file but with unwanted (noisy) data removed, at a specified ppm tolerance. Optionally the deleted molecular weights are shown. It removes those molecular weights 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 data from molecular weights file
Molecular weights file: molwts.dat
Ppm tolerance [50.0]: 
Molecular weights output file [molwts.mwfilter]:

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

Command line arguments 

Filter noisy data from molecular weights file
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     Molecular weights file
   -tolerance          float      [50.0] Ppm tolerance (Any numeric value)
  [-outfile]           outfile    [*.mwfilter] Molecular weights output file

   Additional (Optional) qualifiers:
   -showdel            boolean    [N] Output deleted mwts

   Advanced (Unprompted) qualifiers:
   -datafile           datafile   [Emwfilter.dat] Molecular weight standards
                                  data file

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)		 infile Molecular weights file Input file Required
-tolerance float Ppm tolerance Any numeric value 50.0
[-outfile]
(Parameter 2)		 outfile Molecular weights output file Output file <*>.mwfilter
Additional (Optional) qualifiers
-showdel boolean Output deleted mwts Boolean value Yes/No No
Advanced (Unprompted) qualifiers
-datafile datafile Molecular weight standards data file Data file Emwfilter.dat
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

Input files for usage example

File: 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
backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence
backtranseq Back-translate a protein sequence to a nucleotide sequence
compseq Calculate the composition of unique words in sequences
emowse Search protein sequences by digest fragment molecular weight
freak Generate residue/base frequency table or plot
mwcontam Find weights common to multiple molecular weights files
oddcomp Identify proteins with specified sequence word composition
pepdigest Reports on protein proteolytic enzyme or reagent cleavage sites
pepinfo Plot amino acid properties of a protein sequence in parallel
pepstats Calculates statistics of protein properties
wordcount Count and extract unique words in molecular sequence(s)

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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

None