mwfilter Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. 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 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 (c) 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