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mwfilter |
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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:
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.
% 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
Filter noisy data from molecular weights file
Version: EMBOSS:6.6.0.0
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
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| 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 |
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.
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 |
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:
| 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 | Report on protein proteolytic enzyme or reagent cleavage sites |
| pepinfo | Plot amino acid properties of a protein sequence in parallel |
| pepstats | Calculate statistics of protein properties |
| wordcount | Count and extract unique words in molecular sequence(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.