oracular (1) topdiff.1.gz

Provided by: toppic_1.5.3+dfsg1-1build3_amd64 bug

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)


       Filippo Rusconi and Indiana University-Purdue University Indianapolis