Comet release 2015.01
release 2015.01 rev. 2 (2015.01.2), release date 2015/04/28
- Change decoy generation for E-value calculation when a small number of
candidate peptides are searched. The E-value histogram now includes
3000 decoys, up from hundreds. Decoys fragments are generated from
actual peptides vs. previously "rotating" fragment ions from the
database candidates that were scored. This should improve E-value
calculation for high-res MS/MS searches.
- Modified how the xcorr histogram tail is defined for the E-value calculation.
- Remove low xcorr + low E-value exception. Previously, any peptide with a xcorr
less than 1.0 could not receive a low E-value.
- Fix protein c-terminal modification searches which were not functioning properly.
- Fix cms2 file support which was broken in 2015.01.1.
- Add modification column to text output. The encoding includes position, static or
variable modification, and mass change for each modification in the peptide.
Requested by Noble lab.
- Fix terminal modification reporting in pep.xml header. Reported by D. Hernandez.
- Update MSToolkit to address progress percentage that could go beyond 100%.
Reported by M. Askenazi.
release 2015.01 rev. 1 (2015.01.1), release date 2015/03/06
- Remove some error status checks, implemented for upcoming Windows GUI,
that were severely impacting search performance.
- For direct Thermo .raw file support, update how MSFile Reader library
is referenced. Thanks to C. Grant.
parameter. A value of "2" for this parameter will have Comet ignore all
charge states except for those specified in the
- Known bug: cms2 files not properly supported. Let me know if you need
a binary that supports this input file type.
release 2015.01 rev. 0 (2015.01.0), release date 2015/02/23
- A new the sparse matrix data format implementation
to improve performance. This provides memory savings with no negative
impact on search performance so it's recommended that this parameter should
always be set on. In the next release, this parameter option will likely
go away and the sparse matrix data representation will be on by default
going forward. Implemented by M. Hoopmann.
- For variable modifications, the optional distance constraint can now
be applied to N- and C-termini of peptides in addition to N- and
C-termini of proteins. This allows for proper specification of peptide
terminal mods such as N-terminal glutamine or glutamic acid to pyroglutamate.
- Also, an additional field is present in the variable modification
parameters, for example
to allow the user to be able to force each modification to be present in
- A new parameter
allows one to force analyzed peptides to contain at least
one variable modification. This is different than the field described in
the previous bullet point where any particular variable modification can
be forced to be present. So this new parameter will force the peptide
to be modified with any variable modification whereas the additional
field in the variable modification parameters would force that particular
variable modification) to be present.
- In the Percolator output ("output_percolatorfile"),
the peptide will now use modification characters to denote variable
modifications instead of bracketed masses. For example, "K.M*DLR.T"
instead of "K.M[147.1]DLR.T". Implemented by J. Egertson.
- When using "output_txtfile",
Comet will now report up to
number of hits per spectrum query. Previously Comet would only report
the top hit for the text output. The text output modifications are now
denoted by a mass string (M[147.1]) instead of modification characters (M*).
Note that Comet compiled with the Crux flag turned on already had this
- The search progress reporting now goes from 0% to 100% across batches
for the entire search. Previously it reported search progress of 0% to 100%
within each batch which made it difficult to track overall search progress.
- When reporting the protein name for a peptide, Comet will now report the
protein accession for the first protein in the database that contains
that peptide. Previously, this was not guaranteed when multiple threads
were used in a search.
- In final output, results are sorted by xcorr and then peptide sequence.
Previously, results were only sorted by xcorr. With previous implementation,
searches that had two peptides with the same top xcorr scores could randomly
report either of the two peptides as the top hit. Now the alphabetical
first peptide will always be reported in this scenario (not that the
alphabetical first peptide is any better than the same scoring next
- Change deltaCn reporting. In previous pep.xml output, the deltaCn value was
set to 1.0 for a peptide if
"num_output_lines = 1"
as there is no second hit peptide being reported. This behavior is changed
to calculated the deltaCn against the next best scoring peptide even though
it is not being reported in the output.
- Replaced a constant check in a while loop with a semaphore when checking
queue status for loading sequences to search. Before this change, some
search conditions would cause the CPU usage to be very low due to the
contant while loop check. Implemented by T. Jahan.
- Ability to now search Thermo .raw files directly in Windows. This requires
Thermo's freely available MSFile Reader
library to be installed. Implemented by T. Jahan.
Unfortunately you will need to copy the XRawfile2.dll or XRawfile2_x64.dll
to c:\Windows\MSFileReader.XRawfile2.dll for this to work. Note this is
no longer needed with release 2015.01 rev. 1.
- Change "scannr" to "ScanNr" in the column header line of Percolator output
- Update to MSToolkit version r76: mz5 support removed.
- Known bug: in some (relatively rate) instances of variable modification
searches, the number of duplicate proteins will not be correctly reported.
- Known issue: just ran performance tests (2/25/2015) and discovered that releases
after 2013.02 are slower and do not scale well with the thread count.
Looking into addressing this ASAP.
Documentation for parameters for release 2015.01
can be found here.
Go download from the download page.