Comet releases 2013.01

Documentation for parameters for release 2013.01 can be found here. Download release here.

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' and '-L' 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 scan_range parameter.
• 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. 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.

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