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

1                                                   20200521                                            TOPFD(1)