Comet release 2013.01
release 2013.01 rev 0 (2013.01.0), release date 2013/06/05
- This is the second major release of Comet.
- Comet now supports searching multiple input files i.e. "comet.exe *.mzXML".
Comet will search each input file sequentially, one after the other.
- New command line option '-F<num>' and '-L<num>'
to specify the first and last scan to search. This scan range can also be
specified using the scan_range parameter.
Additionally, the scan range can still be specified appended to
each input file i.e. comet.exe file.mzXML:1500-5000.
Scan ranges specified appended to each mzXML file will override
the -F/-L command line options which in turn will override the
- Fix bug with '-D' command line parameter not applying the specified
sequence database to override the database specified in the params file.
- Fix bug associated with application of use_NL_ions.
An error in the code logic was not applying neutral loss peaks
to all relevant ion series.
- Updated MSToolkit code for more robust reading of input files.
- New parameter: use_sparse_matrix
Implemented by Mike Hoopman, the main new feature of
Comet release 2013.01 is the ability to use a sparse matrix
data representation internally.
When using a small fragment_bin_tol value (i.e. 0.01), the original
implementation of Comet will use a *huge* amount of memory (see
the memory use table here).
The sparse matrix implementation reduces memory use tremendously
but searches are slower than the classical implementation.
- New parameter: spectrum_batch_size
This parameter defines how many spectra are searched at
a time. For example, if the parameter value were set to 1000 then
Comet would loop through searching about 1000 spectra at a time until
all data are analyzed. This can be used for searching a large dataset
that might not fit in memory when searched all at once.
- New parameter: clear_mz_range
This parameter removes (i.e. clears out) all peaks within the
specified m/z range prior to any data processing and searching.
This functionality was intended for iTRAQ/TMT type analysis with
the goal to ignore the reporter ion signals from the search.
- Revised parameter: fragment_bin_offset
In the 2012.01 release, the valid value of this parameter
ranged from 0.0 to the fragment_bin_tol value. Per request,
the meaning of this parameter has been changed such that valid
values now range from 0.0 to 1.0 where the actual offset value
scales by fragment_bin_tol. This is not a parameter that most
users should care about; use the recommended values written in
the params file notes.
- Add version number to head of comet.params file.
Comet will now validate that a compatible params file is
being used by checking the version number written in the comet.params
file. This was added to avoid running Comet using an old/outdated
parameters file where an existing parameter name might have a change
in behavior (such as fragment_bin_offset above). Comet will not
run if the version string is not compatible.
- Change format of output filenames when input scan range is specified.
When searching a scan range, say 1-5000, release 2012.01
would create output files with the name extension basename.pep.xml:1-5000
or basename.sqt:1-5000. This version 2013.01 will now name these
files as basename.1-5000.pep.xml and basename.1-5000.sqt. This
keeps the file extensions (.pep.xml and .sqt) at the end of the
filenames for better compatibility with downstream tools.
Ideally one uses the spectrum_batch_size
parameter and not run individual subset scan range searches to
avoid this naming issue.
Documentation for parameters for release 2013.01
can be found here.
For low-res ms/ms spectra, try the following settings:
- fragment_bin_tol = 1.0005
- fragment_bin_offset = 0.4
- theoretical_fragment_ions = 1
For high-res ms/ms spectra, try the following settings:
- fragment_bin_tol = 0.02
- fragment_bin_offset = 0.0
- theoretical_fragment_ions = 0
Go download from the download link.