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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
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
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 standard output
-filter boolean Read standard input, write 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. 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
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 codons
backtranseq Back translate a protein sequence
charge Protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
compseq Count 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 (ajb ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, 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
None
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