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
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. 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
|Standard (Mandatory) qualifiers||Allowed values||Default|
|Molecular weights file||Input file||Required|
|-tolerance||Ppm tolerance||Any numeric value||50.0|
|Molecular weights output file||Output file||<*>.mwfilter|
|Additional (Optional) qualifiers||Allowed values||Default|
|-showdel||Output deleted mwts||Boolean value Yes/No||No|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
|-datafile||Molecular weight standards data file||Data file||Emwfilter.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.
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:
|backtranambig||Back-translate a protein sequence to ambiguous nucleotide sequence|
|backtranseq||Back-translate a protein sequence to a nucleotide sequence|
|charge||Draw a protein charge plot|
|checktrans||Reports STOP codons and ORF statistics of a protein|
|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|
|iep||Calculate the isoelectric point of proteins|
|mwcontam||Find weights common to multiple molecular weights files|
|octanol||Draw a White-Wimley protein hydropathy plot|
|pepinfo||Plot amino acid properties of a protein sequence in parallel|
|pepstats||Calculates statistics of protein properties|
|pepwindow||Draw a Kyte-Doolittle hydropathy plot for a protein sequence|
|pepwindowall||Draw Kyte-Doolittle hydropathy plot for a protein alignment|
|wordcount||Count and extract unique words in DNA sequence(s)|