NAME

       topdiff  -  Top-down  mass  spectrometry-based  identification of Differentially expressed
       proteoforms

SYNOPSIS

          topdiff [options] database-file-name spectrum-file-names

DESCRIPTION

       TopDiff (Top-down  mass  spectrometry-based  identification  of  Differentially  expressed
       proteoforms)  compares  the  abundances  of proteoforms and finds differentially expressed
       proteoforms by using identifications of top-down mass spectrometry data of several protein
       samples.

       1. Input

             • A protein database file in the FASTA format

             • Several mass spectrum data files in the msalign format

             • Proteoform identification files of the mass spectrum data files in the xml format,
               e.g., spectra_ms2_toppic_proteoform.xml

       2. Output

          TopDiff outputs a csv file containing proteoform identifications and  their  abundances
          in the input mass spectrum data. The default output file name is sample_diff.csv.

OPTIONS

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

       -f  [  --fixed-mod  ]  <C57|C58|a  fixed modification file> Set fixed modifications. Three
       available options: C57, C58, or the name of a text  file  specifying  fixed  modifications
       (see  an example file). When C57 is selected, carbamidomethylation on cysteine is the only
       fixed modification. When C58 is selected, carboxymethylation on cysteine is the only fixed
       modification.

       -e  [  --error-tolerance  ]  <a  positive  number>  Set  the  error  tolerance for mapping
       identified proteoforms across multiple samples (in Dalton). Default value: 1.2 Dalton.

       -t [ --tool-name ] <toppic|topmg> Specify the name of the database search tool: toppic  or
       topmg. Default: toppic.

       -o [ --output ] <a file name> Specify the output file name. Default: sample_diff.csv.

EXAMPLES

       • Compare  proteoform  abundances  using  TopPIC  identifications  of  two  spectrum files
         spectra1_ms2.msalign and spectra2_ms2.msalign. The protein sequence database  file  name
         is proteins.fasta.

         topdiff proteins.fasta spectra1_ms2.msalign spectra2_ms2.msalign

       • Compare  proteoform  abundances  using  TopPIC  identifications  of  two  spectrum files
         spectra1_ms2.msalign and spectra2_ms2.msalign. The protein sequence database  file  name
         is proteins.fasta and a fixed modification, carbamidomethylation on cysteine, is used in
         database search.

         topdiff -f C57 proteins.fasta spectra1_ms2.msalign spectra2_ms2.msalign

       • Compare  proteoform  abundances  using  TopMG  identifications  of  two  spectrum  files
         spectra1_ms2.msalign  and  spectra2_ms2.msalign. The protein sequence database file name
         is proteins.fasta and a fixed modification, carbamidomethylation on cysteine, is used in
         database search.

         topdiff -f C57 -t topmg proteins.fasta spectra1_ms2.msalign spectra2_ms2.msalign

SEE ALSO

       • topfd (1)

       • toppic (1)

       • topmg (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