NAME

       topfd - Top-down mass spectral Feature Detection

SYNOPSIS

          topfd [options] spectrum-file-names

DESCRIPTION

       TopFD  (Top-down mass spectral Feature Detection) is a software tool for top-down spectral
       deconvolution, which groups top-down mass spectral peaks  into  isotopomer  envelopes  and
       converts  isotopomer  envelopes  to  monoisotopic neutral masses. In addition, it extracts
       proteoform features from MS1 spectra.

       1. Input

          The input of TopFD is mass spectrometry data files in the mzXML  or  mzML  format.  Raw
          mass  spectral  data generated from various mass spectrometers can be converted to mzML
          or mzXML files using msconvert.

       2. Output

          TopFD outputs two LC/MS feature text files with a file extension "feature",  one  LC/MS
          feature  file  with  a file extension "xml", and a deconvoluted mass spectral data file
          for MS/MS spectra in the msalign format with  a  file  extension  "msalign",  which  is
          similar  to the MGF file format. In addition, TopFD creates two folders containing java
          scripts files of spectral data for spectral visualization and other files generated  in
          spectral  deconvolution.   For  example,  when the input file name is spectra.mzML, the
          output includes:

             • spectra_ms1.feature: a feature file containing LC/MS features.

             • spectra_ms2.feature:  a  feature  file  containing  MS/MS  scan  IDs   and   their
               corresponding LC/MS feature IDs.

             • spectra_feature.xml: a feature file containing LC/MS features in the xml format.

             • spectra_ms2.msalign: a list of deconvoluted MS/MS spectra.

             • spectra_file:  a  folder  containing  deconvoluted  MS1 spectra and annotations of
               LC/MS data.

             • spectra_html: a folder containing java script files of  MS1  and  MS/MS  data  for
               spectral visualization.

OPTIONS

       -h [ --help ] Print the help message.

       -c  [  --max-charge  ]  <a positive integer> Set the maximum charge state of precursor and
       fragment ions. The default value is 30.

       -m [ --max-mass ] <a positive number> Set the maximum monoisotopic mass of  precursor  and
       fragment ions. The default value is 100,000 Dalton.

       -e  [  --mz-error  ] <a positive number> Set the error tolerance of m/z values of spectral
       peaks. The default value is 0.02 m/z.

       -r [ --ms-one-sn-ratio ] <a positive number> Set the signal/noise ratio for  MS1  spectra.
       The default value is 3.

       -t [ --ms-two-sn-ratio ] <a positive number> Set the signal/noise ratio for MS/MS spectra.
       The default value is 1.

       -w [ --precursor-window ] <a positive number> Set the precursor isolation window size. The
       default value is 3.0 m/z.

       -o [ --missing-level-one ] Specify that the input file does not contain MS1 spectra.

EXAMPLES

       • Deconvolute    a    centroid   data   file   spectra.mzML   and   output   four   files:
         spectra_ms2.msalign, spectra_ms1.feature, spectra_ms2.feature, spectra_feature.xml.

         topfd spectra.mzML

       • Deconvolute two centroid data files spectra1.mzML and  spectra2.mzML  and  output  three
         files for each input data file.

         topfd spectra1.mzML spectra2.mzML

       • Deconvolute all centroid data files in the current folder.

         topfd *.mzML

       • Deconvolute a centroid data file spectra.mzML that does not contain MS1 spectra.

         topfd -o spectra.mzML

       • Deconvolute  a  centroid data file spectra.mzML with a precursor isolation window size 2
         m/z.

         topfd -w 2 spectra.mzML

       • Deconvolute a centroid data file spectra.mzML  with  a  signal/noise  ratio  2  for  MS1
         spectra.

         topfd -r 2 spectra.mzML

       • Deconvolute  a  centroid data file spectra.mzML with the following settings: the maximum
         charge state: 50, the maximum mass: 30,000 Dalton, and the signal/noise ratio for  MS/MS
         spectra: 2.

         topfd -c 50 -m 30000 -t 2 spectra.mzML

SEE ALSO

       • toppic (1)

       • topmg (1)

       • topdiff (1)

MAN PAGE PRODUCTION

       This man page was written by Filippo Rusconi <lopippo@debian.org>. Material was taken from
       http://proteomics.informatics.iupui.edu/software/toppic/manual.html.

AUTHOR

       Filippo Rusconi <lopippo@debian.org> and  upstream  authors  (Dr.  Xiaowen  Liu's  Lab  at
       Indiana University-Purdue University Indianapolis and others)

COPYRIGHT

       Filippo Rusconi and Indiana University-Purdue University Indianapolis