Provided by: toppic_1.5.3+dfsg1-1_amd64 bug

NAME

       toppic - Top-down mass spectrometry based Proteoform Identification and Characterization

SYNOPSIS

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

DESCRIPTION

       TopPIC  (Top-down  mass spectrometry based Proteoform Identification and Characterization)
       identifies and characterizes proteoforms at  the  proteome  level  by  searching  top-down
       tandem  mass  spectra  against  a  protein  sequence  database.   TopPIC is a successor to
       MS-Align+. It efficiently identifies proteoforms  with  unexpected  alterations,  such  as
       mutations   and   post-translational   modifications   (PTMs),  accurately  estimates  the
       statistical significance of identifications, and characterizes reported  proteoforms  with
       unknown  mass  shifts.  It  uses  several techniques, such as indexes, spectral alignment,
       generation function methods, and  the  modification  identification  score  (MIScore),  to
       increase the speed, sensitivity, and accuracy.

       1. Input

             • A protein database file in the FASTA format

             • A mass spectrum data file in the msalign format

             • A text file containing LC/MS feature information (optional)

             • A text file of fixed PTMs (optional)

             • A text file of PTMs for the characterization of unexpected mass shifts (optional)

       2. Output

       TopPIC  outputs  two  comma  separated value (csv) files, an xml file, and a collection of
       html files  for  identified  proteoforms.  For  example,  when  the  input  data  file  is
       spectra_ms2.msalign, the output includes:

          • spectra_ms2_toppic_prsm.csv:    a   csv   file   containing   identified   proteoform
            spectrum-matches (PrSMs) with an E-value or spectrum level FDR cutoff.

          • spectra_ms2_toppic_proteoform.csv: a csv file containing identified proteoforms  with
            an E-value or proteoform level FDR cutoff.

          • spectra_ms2_toppic_proteoform.xml: an xml file containing identified proteoforms with
            the E-value or proteoform level FDR cutoff.

          • spectra_html/toppic_prsm_cutoff: a folder containing java script files of  identified
            PrSMs using the E-value or spectrum level FDR cutoff.

          • spectra_html/toppic_proteoform_cutoff:  a  folder  containing  java  script  files of
            identified PrSMs using the E-value or proteoform level FDR cutoff.

          • spectra_html/topview: a  folder  containing  html  files  for  the  visualization  of
            identified PrSMs.

       To  browse  identified  proteins, proteoforms, and PrSMs, use a chrome browser to open the
       file spectrum_html/topview/index.html. Google Chrome is recommended (Firefox  and  IE  are
       not recommended).

       When the input contains two or more data files, TopPIC outputs two csv files, an xml file,
       and a collection of html files for each input file. When a  file  name  is  specified  for
       combined  identifications,  it  combines  spectra  and proteoforms identified from all the
       input files, removes redundant proteoform identifications, and reports two csv  files,  an
       xml  file,  and a collection of html files for the combined results. For example, when the
       input is spectra1_ms2.msalign and spectra2_ms2.msalign and the combined output  file  name
       is "combined," the output files are:

          • combined_ms2_toppic_prsm.csv:  a  csv  file  containing PrSMs identified from all the
            input files with an E-value or spectrum level FDR cutoff.

          • combined_ms2_toppic_proteoform.csv: a csv file containing proteoforms identified from
            all the input files with an E-value or proteoform level FDR cutoff.

          • combined_ms2_toppic_proteoform.xml:  an  xml  file  containing proteoforms identified
            from all the input files with the E-value or proteoform level FDR cutoff.

          • combined_html/toppic_prsm_cutoff: a folder containing  java  script  files  of  PrSMs
            identified from all the input files using the E-value or spectrum level FDR cutoff.

          • combined_html/toppic_proteoform_cutoff:  a  folder  containing  java  script files of
            PrSMs identified from all the input files using the E-value or proteoform  level  FDR
            cutoff.

          • combined_html/topview:  a  folder  containing  html  files  for  the visualization of
            identified PrSMs.

OPTIONS

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

       -a [ --activation ] <CID|HCD|ETD|UVPD|FILE>  Set  the  fragmentation  method(s)  of  MS/MS
       spectra.  When  "FILE"  is selected, the fragmentation methods of spectra are given in the
       input spectrum data file. Default value: FILE.

       -f [ --fixed-mod ] <C57|C58|a fixed modification  file>  Set  fixed  modifications.  Three
       available  options:  C57,  C58,  or  the name of a text file containing the information of
       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.

       -n [ --n-terminal-form ] <a list of allowed N-terminal  forms>  Set  N-terminal  forms  of
       proteins.  Four  N-terminal  forms  can  be  selected:  NONE,  NME,  NME_ACETYLATION,  and
       M_ACETYLATION. NONE stands for no modifications, NME for N-terminal  methionine  excision,
       NME_ACETYLATION  for N-terminal acetylation after the initiator methionine is removed, and
       M_ACETYLATION for N-terminal methionine acetylation. When multiple forms are allowed, they
       are separated by commas. Default value: NONE,M_ACETYLATION,NME,NME_ACETYLATION.

       -d  [  --decoy ] Use a shuffled decoy protein database to estimate spectrum and proteoform
       level FDRs. When -d is chosen, a shuffled decoy database is  automatically  generated  and
       appended  to the target database before database search, and FDR rates are estimated using
       the target-decoy approach.

       -e [ --mass-error-tolerance ] <a positive integer> Set the error tolerance  for  precursor
       and  fragment  masses  in part-per-million (ppm). Default value: 15. When the lookup table
       approach (-l) is used for E-value estimation, valid error tolerance values are 5, 10,  and
       15 ppm.

       -p  [  --proteoform-error-tolerance  ]  <a  positive  number>  Set the error tolerance for
       identifying PrSM clusters (in Dalton). Default value: 1.2 Dalton.

       -M [ --max-shift ] <a number> Set  the  maximum  value  for  unexpected  mass  shifts  (in
       Dalton). Default value: 500.

       -m [ --min-shift ] <a number> Se the minimum value for unexpected mass shifts (in Dalton).
       Default value: -500.

       -s [ --num-shift ] <0|1|2> Set the maximum number of unexpected mass  shifts  in  a  PrSM.
       Default value: 1.

       -t  [  --spectrum-cutoff-type  ]  <EVALUE|FDR>  Set  the  spectrum  level  cutoff type for
       filtering PrSMs. Default value: EVALUE.

       -v [ --spectrum-cutoff-value ] <a positive number> Set the spectrum level cutoff value for
       filtering PrSMs. Default value: 0.01.

       -T  [  --proteoform-cutoff-type  ]  <EVALUE|FDR>  Set the proteoform level cutoff type for
       filtering proteoforms and PrSMs. Default value: EVALUE.

       -V [ --proteoform-cutoff-value ] <a positive number> Set the proteoform level cutoff value
       for filtering proteoforms and PrSMs. Default value: 0.01.

       -l [ --lookup-table ] Use a lookup table method for computing p-values and E-values. It is
       faster than the default generating function approach, but it  may  reduce  the  number  of
       identifications.

       -r [ --num-combined-spectra ] <a positive integer> Set the number of combined spectra. The
       parameter is set to 2 (or 3) for combining spectral pairs (or triplets) generated  by  the
       alternating fragmentation mode. Default value: 1.

       -i  [ --mod-file-name ] <a common modification file> Specify a text file containing a list
       of common PTMs for proteoform characterization. The PTMs are used to identify and localize
       PTMs in reported PrSMs with unknown mass shifts. See an example file.

       -H  [  --miscore-threshold  ] <a number between 0 and 1> Set the score threshold (MIScore)
       for filtering results of PTM characterization. Default value: 0.45.

       -u [ --thread-number ] <a  positive  number>  Set  the  number  of  threads  used  in  the
       computation.  Default value: 1. The maximum number of threads is determined by the CPU and
       memory of the computer used for computation. About  4  GB  memory  is  required  for  each
       thread.  If  the  computer  has 16 GB memory and a CPU with 8 cores, the maximum number of
       threads is 4 because about 16 GB memory is needed for 4 threads.

       -x [ --no-topfd-feature ] Specify that there are no TopFD  feature  files  for  proteoform
       identification.

       -c  [  --combined-file-name  ]  <a  filename>  Specify  an  output  file name for combined
       identifications when the input consists of multiple spectrum files.

       -k [ --keep ] Keep intermediate files generated by TopPIC.

EXAMPLES

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file  proteins.fasta  with  a  feature  file  spectra.feature. The user does not need to
         specify the feature file name. TopPIC will automatically obtain  the  names  of  feature
         files from the spectrum file name spectra_ms2.msalign.

         toppic proteins.fasta spectra_ms2.msalign

       • Search    two    deconvoluted    MS/MS    spectrum    files   spectra1_ms2.msalign   and
         spectra2_ms2.msalign against a protein database file proteins.fasta with feature  files.
         In addition, all identifications are combined and reported using a file name "combined."

         toppic -c combined proteins.fasta spectra1_ms2.msalign spectra2_ms2.msalign

       • Search  all  deconvoluted  MS/MS  spectrum files in the current folder against a protein
         database file proteins.fasta with feature files.

         toppic proteins.fasta *_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta without feature files.

         toppic -x proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files and a fixed modification: carbamidomethylation on
         cysteine.

         toppic -f C57 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. In an identified  proteoform,  at  most  2  mass
         shifts are allowed and the maximum allowed mass shift value is 10,000 Dalton.

         toppic -s 2 -M 10000 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. The error tolerance for precursor  and  fragment
         masses is 5 ppm.

         toppic -e 5 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature  files.  Use  the  target  decoy  approach  to  compute
         spectrum  level and proteoform level FDRs, filter identified proteoform spectrum-matches
         by a 5% spectrum level FDR, and filter identified proteoforms by a 5%  proteoform  level
         FDR.

         toppic -d -t FDR -v 0.05 -T FDR -V 0.05 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign with alternating CID, HCD,
         and ETD spectra against a protein  database  file  proteins.fasta  with  feature  files.
         Combine alternating CID, HCD, and ETD spectra to increase proteoform coverage.

         toppic -r 3 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. After proteoforms with  unexpected  mass  shifts
         are  identified,  TopPIC  matches  the  mass  shifts  to  four common PTMs: acetylation,
         phosphorylation, oxidation and methylation, and uses an MIScore  cutoff  0.3  to  filter
         reported PTM sites. The modification file common_mods.txt can be found here.

         toppic -i common_mods.txt -H 0.3 proteins.fasta spectra_ms2.msalign

       • Search a deconvoluted MS/MS spectrum file spectra_ms2.msalign against a protein database
         file proteins.fasta with feature files. Use 6 CPU threads to speed up the computation.

         toppic -u 6 proteins.fasta spectra_ms2.msalign

SEE ALSO

       • topfd (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