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mwfilter |
Function
Filter noisy molwts from mass spec outputDescription
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 weight file input: 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
Standard (Mandatory) qualifiers:
[-infile] infile Molecular weight file input
-tolerance float Ppm tolerance
[-outfile] outfile Output file name
Additional (Optional) qualifiers:
-showdel boolean Output deleted mwts
Advanced (Unprompted) qualifiers:
-datafile datafile Data file of noisy molecular weights
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 deaths
|
| Standard (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 |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -showdel | Output deleted mwts | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -datafile | Data file of noisy molecular weights | Data file | Emwfilter.dat |
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 |
|---|---|
| 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