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<title>Release notes for Crux</title>
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<h2>Release notes for Crux</h2>
<h4>Minor changes</h4>
<ul>
<li>19 Feb 2023: Add a "filename" column to the Percolator tab-delimited output files.</li>
<li>07 Feb 2023: bug fix in mix-max procedure. qvalues are now the smallest fdrs
for associated thresholds. </li>
<li>13 Jan 2023: tide-search halts halts with an error message when the user tries
to use tailor-calibration in conjunction with peptide-centric search. </li>
<li>13 Jan 2023: Added a check to verify that these release notes are
updated in every pull request.</li>
<li>09 Jan 2023: Upgraded to Comet 2022.01 rev 2. Fixed issue #572: handling of
Comet isotope_error option (now allows values 0-5).</li>
<li>04 Jan 2023: Fix divide-by-zero bug in postprocessing diameter results.</li>
<li>16 Dec 2022: Changed the default precision for specifying
variable modifications to four decimal points rather than two.</li>
<li>13 Dec 2022: Updated to Kojak commit 4307dfa from Oct 11 2022 and
MSToolkit commit 20e99ce from Sept. 14 2022.
Added NeoPepXMLParser commit e89f166 from Jul 1 2022 as an external dependency.</li>
<li>15 Oct 2022: The percolator command no longer creates mzIdentML
output, and the tab-delimited text format produced by crux percolator
now mimics that of the stand-alone version of Percolator. The crux
spectral-counts and assign-confidence commands have been updated
to parse the new percolator output files.Updated to percolator committ 879af86.</li>
<li>28 Sept 2022: Updated Assign-confidence to the new comet output. </li>
<li>28 Sept 2022: Updated performance and smoke tests </li>
<li>28 Sept 2022: Added option to tide-search to search spectra in a min- and max-precursor-charge range. </li>
<li>28 Sept 2022: Removed the option from tide-index to generate decoy protein fasta file.</li>
<li>28 Sept 2022: Fixed bug in tide index which prevented it generating terminal variable modifications.</li>
<li>28 Sept 2022: Fixed bug in tide index which slowed it down when generating many mods.</li>
<li>22 Aug 2022: The scalability of tide-index has been improved to allow for creation
of very large peptide databases. This is done by sorting and filtering the peptides on
disk rather than in memory. A new parameter, --memory-limit, allows the user to specify
an upper bound on the memory (i.e. RAM) usage of tide-index. Note that this update
required that the data structure used in Tide's index files has changed. It is therefore
recommended that users' recreate old index files. Currently, indices in the old format
can still be used with tide-index, but this format may be deprecated in future releases
of Crux.</li>
<li>17 August 2022: Updated to percolator committ 1e82daa.</li>
<li>27 July 2022: Fixed bug preventing percolator from running on Kojak output.</li>
<li>19 July 2022: Added min_peptide_score parameter to Kojak. </li>
<li>09 June 2022: Upgraded to ProteoWizard 3.0.22014 (commit aadd392). This
also upgrades to BOOST 1.67 which fixes a problem building Crux on current MacOS
systems.</li>
<li>Upgraded to Protocol Buffers 3.19.4</li>
<li>Upgraded to GFlags 2.2.2</li>
<li>09 June 2022: Added support for building using GitHub Actions.</li>
<li>01 May 2022: XCorr scoring implementing in C++. This resolves a
longstanding bug in our multithreading code. </li>
<li>20 Jan 2022: The XCorr scoring, exact p-value, and ResEv in Tide-Search has been sped up. </li>
<li>10 Jan 2022: Fixed bug that resulted in rank=0 for search results in pepxml files (issue #521).</li>
<li>16 Nov 2021: The preprocessing of the exact p-value method has been aligned to the preprocessing of the standard XCorr scoring. </li>
<li>16 Nov 2021: Comet has been upgraded to version 2021.01.0.</li>
<li>16 Nov 2021: Kojak has been upgraded to commit defa8c9.</li>
<li>16 Nov 2021: MSToolkit has been upgraded to commit 4cb705d.</li>
<li>16 Nov 2021: IUPAC symbol 'O' is now the amino acid pyrrolysine.</li>
<li>16 Nov 2021: Dropped support for 32-bit versions of Crux.</li>
<li>9 Nov 2021: Fix the crash bug in <code>diameter</code> when there is no MS1 spectrum in the input file. </li>
<li>5 Nov 2021: Update the param-medic documentation to include
pointers to published papers and to describe detection of modifications.</li>
<li>30 Oct 2021: Remove the protein-reverse option from "--decoy-format" in <code>tide-index</code> and <code>generate-peptides</code>. </li>
<li>23 Oct 2021: Revised the <code>tide-index</code> so that "--peptide-list T" will generate a single text file listing of all the peptides in the database, along with their corresponding decoy peptides, neutral masses and proteins, one per line. </li>
<li>18 Oct 2021: Fixed a bug in DIAmeter that caused it to detect 0 PSMs when the <code>windowWideness</code> property is missing in the input file. </li>
<li>18 Oct 2021: Revised the DIAmeter documentation to clarify which options are affected by the setting of <code>diameter-instrument</code>. </li>
</ul>
<hr/>
<h3>Version 4.1</h3> October Oct. 11, 2021
<h4>Major changes</h4>
<ul>
<li>06 Oct 2021: Added DIAmeter module for searching for detecting peptides from data-independent acquisition mass spec data without requiring a spectral library.
The methodology is described in<br/>
<a href="https://doi.org/10.1093/bioinformatics/btab284"/>
Lu et al. Bioinformatics 37(Supplement_1):i434–i442, 2021</a>.
</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>14 Sept 2021: Add second set of smoke-tests that give tide-search a FASTA file instead of a database index.</li>
<li>14 Sept 2021: Replace contents of demo.ms2 in the tutorials with new data (bug #454).</li>
<li>10 Jun 2021: Fixed bug in computing the m/z window size in
Tide. Affected only the setting when <code>precursor-window-type=mz</code>.</li>
<li>7 Jun 2021: Revised documentation and added check to ensure that
the brief-output option to tide-search is not used in conjunction
with formats other than tab-delimited text output.</li>
<li>11 May 2021: Fixed bug in p-value search that incorrectly set the bin_width to 0 when tide-search was given a FASTA file.</li>
<li>11 May 2021: Added smoke tests to test case where tide-search is given a FASTA file instead of a index.</li>
</ul>
<hr/>
<h3>Version 4.0</h3> April 06, 2021
<h4>Major changes</h3>
<ul>
<li>Mar. 9, 2021: Removed seldom used commands: xlink, xlink-assign-ions, xlink-score-spectrum,
barista, q-ranker, extract-columns, extract-rows, stat-column, sort-by-column.
</li>
<li>Nov. 6, 2020: Updated to use Comet 2019.05.</li>
<li>Nov. 6, 2020: Added Kojak module for searching for cross-linked peptides.
The methodology is described in<br/>
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428575"/>
Hoopmann et al. Journal of Proteome Research, 2015</a>.
</li>
<li>July 23, 2019: Added the Tailor PSM score calibration method to Tide-search as
an option.
</li>
<li>June 4, 2019: The Crux automatic build process was modified to use a cached version
of the Proteowizard source, rather than always using the latest version available.
The current cached version is Proteowizard 3.0, Git commit c172999.
You can configure the Crux build to use the most recent available
Proteowizard source code by passing the option
-DUSE_LATEST_PWIZ=ON on the CMake command line.
</li>
<li>
April 23, 2019: Updated Param-Medic to enable inference of the
presence of various types of modifications, including
stable-isotope and isobaric labeling and tandem mass tags as well
as the enrichment of phosphorylated peptides. The methodology is
described in
<a href="https://pubs.acs.org/doi/full/10.1021/acs.jproteome.8b00954">May
et al. Journal of Proteome Research, 2019</a>.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
Mar 10, 2021: Changed num-threads default to 1.
</li>
<li>
Feb. 12, 2021: Added date of latest commit to version string.
</li>
<li>
Feb. 11, 2021: Fixed bug in support for comet. Output files were
being stored in the wrong directory when multiple spectra files
were provided.
</li>
<li>
Feb 9, 2021: Added process ID number to the names of temporary
files created by Tide, to avoid conflicts.</li>
<li>
Jan. 11, 2021: Fixed break in build of Percolator.
</li>
<li>
December 7, 2020: Updated documentation to remove "+" from the usage statement.
</li>
<li>
December 4, 2020: Updated schematic diagram of Crux tools.
</li>
<li>
December 3, 2020: Fixed bug in peptide-centric search that caused
mis-scaling of XCORR score on some Linux systems.
</li>
<li>
September 16, 2020: Add an additional parser to parse scan number out of the “TITLE” line in MGF files. Now the TITLE line can consist of two formats. The first format is TITLE=fileName.scanNumber.scanNumber.charge.dta. The second format is TITLE=fileName.scanNumber.scanNumber.charge File:"fileNameWithExtension", NativeID:"controllerType=0 controllerNumber=1 scan=scanNumber"
</li>
<li>
Sept. 18, 2020: Updated MGF file parser to handle title line.
</li>
<li>
August 28, 2020: Updated documentation for --use-neutral-loss-peaks.
</li>
<li>
August 27, 2020: Added support for protein terminal modifications. See <a href="faq.html">FAQ page</a> for details.
</li>
<li>
August 7, 2020: Added --lysarginase as an enzyme option to tide-index
and generate-peptides. The rule this enzyme follows is [ ]:[KR].
</li>
<li>
May 28, 2020: Added fixes for pepXML schema validation failures.
</li>
<li>
April 28, 2020: Added the --brief-output option to tide-search,
which prints only a subset of fields to the output file.
</li>
<li>
April 27, 2020: Fixed build of Percolator to use BLAS libraries.
</li>
<li>
March 18, 2020: Crux now builds MSTookit from original repository
rather than a fork.
</li>
<li>
December 16, 2019: Fixed a bug in Tailor method where minimal number of candidate
peptides were selected incorrectly.
</li>
<li>
October 18, 2019: Added res-ev p-value to performance-test. Fixed a bug in assign-confidence
where columns were incorrectly shown when res-ev p-value was used as the score function.
</li>
<li>
October 16, 2019: Fixed a bug in spectral-counts where the first amino acid
of a peptide was be ignored if the flanking amino acids were unavailable.
</li>
<li>
October 1, 2019: Added the "--static" option for percolator to enable the
use of pretrained, static models.
</li>
<li>
July 24, 2019: Fixed a bug in tide-search where delta_cn and delta_lcn were not
correctly calculated for the following score functions: res-ev, res-ev p-value, and
combined p-value.
</li>
<li>
June 19, 2019: Fixed a couple of bugs in the calculation of residue-evidence
and res-ev p-value. Correctly released memory when determining amino acid frequency.
Added a bounds check when adding evidence to the residue-evidence matrix.
Previously when calculating residue-evidence, all fragment ions were considered to be
1+ or 2+. Now fragment ions are only considered to be 2+ when the precursor charge
is at least 2.
</li>
<li>
April 16, 20219: Fixed Windows path parsing bug in spectral-counts.
</li>
<li>
April 11, 2019: Changed the default parameters for tide-search so
that the default mz bin width is 0.02 Da instead of 1.0005079 Da
and the default precursor mass window is 50 ppm, rather
than the previous default of 3 Da.
</li>
<li>
November 6, 2018: Decoy generation will now allow duplicate decoy peptides
within a decoy database and bewteen decoy databases.
</li>
<li>
September 18, 2018: Modified the custom-enzyme flag to tide-index
so that {X} can be used to indicate that all amino acids prevent
cleavage. This is useful when providing a pre-digested set of
peptides as input to tide-index.
</li>
<li>
September 10, 2018: Fixed a bug in the calculation of the lnrSp
feature in make-pin. Previously, the code took the log of the
rank, indexed from zero. To avoid taking the log of zero, the
code inserted the value zero when the rank was equal to zero. The
effect was that both rank 0 and rank 1 received the same lnrSp
score (i.e., zero). The fix is to do the calculation with rank
indexed from one instead of zero.</li>
<li>
August 22, 2018: Fixed a bug causing filenames to be blank in
Percolator outputs.</li>
<li>
August 14, 2018: Improved handling for terminal modifications when
parsing peptide sequences.</li>
<li>
July 17, 2018: Added a hidden option called "use-old-atdc" to the
assign-confidence command. This is included to allow comparison of
the originally published version of aTDC with the new-and-improved
version.</li>
<li>
July 16, 2018: Fixed a bug in how decoys are generated in
tide-index. An off-by-one indexing problem led to some decoys
being erroneously skipped even if they were not actually
duplicates.</li>
<li>
June 19, 2018: Updated comet to release 2018012.</li>
<li>
May 30, 2018: Fixed a bug in spectral-counts that affected how the
parsimony flag reported peptide ranks.</li>
</ul>
<hr/>
<h3>Version 3.2.x</h3> June 19, 2018
<h4>Major changes</h4>
<ul>
<li>
Crux on Linux now requires v 2.17 or higher of the C runtime libraries.
</li>
<li>Building Crux on Windows now requires Visual Studio 2017</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>Fixed documentation errata</li>
<li>Disabled network access by Comet</li>
<li>Updated to Comet 2018012</li>
<li>A 32-bit Linux version of Crux can be built on 64-bit Linux machines.</li>
<li>Added support for parsing UNIMOD modifications.</li>
</ul>
<h3>Version 3.2</h3> May 20, 2018
<h4>Major changes</h4>
<ul>
<li>
Added the residue-evidence (res-ev), residue-evidence p-value
(res-ev p-value), and combined p-value score
functions to tide-index and cascade-search, and modified
assign-confidence and percolator to handle these score
functions. More details are available in
<a href="https://www.biorxiv.org/content/early/2018/03/30/290858">"Combining
high resolution and exact calibration to boost statistical power: A
well-calibrated score function for high-resolution MS2
data"</a>.</li>
<li>
Implemented the "average target-decoy competition" protocol
in <code>assign-confidence</code>. More details are available in
<a href="https://link.springer.com/chapter/10.1007/978-3-319-56970-3_7">"Progressive
calibration and averaging for tandem mass spectrometry statistical
confidence estimation: Why settle for a single decoy?"</a>.</li>
<li>
Added the localize-modification command to find the most likely locations
of post-translational modifications on peptides from a set of
peptide-spectrum matches.</li>
<li>
Improved handling of modifications in tide-index, allowing for indices
containing many different types of modifications.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
Added 'equal-I-and-L' option to tide-index and spectral-counts commands.
This directs the commands to treat I and L as equivalent amino acids. </li>
<li>
Percolator and make-pin can now accept multiple files on the
command line.</li>
<li>
Updated Comet to version 2018.01 rev. 0.</li>
<li>
Implemented improvements to I/O speed for MzIdent format.</li>
<li>
Crux distributions are now identified using an abbreviated unique
string from the version control system.</li>
<li>
Added support for mzML to qranker and barista.</li>
<li>
Modified tide-search to reports peak counts separately for each
thread.</li>
<li>
Added "deisotope" option to tide-search.</li>
<li>
Added "max-charge-feature" option to make-pin so
that the user can control how many charge features are
created.</li>
<li>
Improved tide-index so that it will automatically recognize when
too many temporary files will be required and to index modified
peptides using an alternate method.</li>
<li>
Added the "mod-precision" option to control the
number of digits used to represent post-translational
modifications in various output files.</li>
<li>
Modified cascade-search so that the q-value threshold is not
applied to the final database in the cascade.</li>
<li>
Tide-index will now clip methionines at the begining of proteins that do
not have an internal clevage site.</li>
<li>
Enabled search-for-xlinks to search multiple spectra files,
in any of the file formats supported by Proteowizard. Support for the
<code>file-column</code> option added.</li>
<li>
Added the print-progress, concat, and mono-link options to
search-for-xlinks and simplified the mod option.</li>
<li>
Changed the tide-search precursor-window option upper bound from
100 to 1,000,000,000 to allow open modification searching.</li>
<li>
Added PepXML support for mod_nterm_mass and mod_cterm_mass on
modification_info.</li>
<li>
Removed the <code>feature-file-in</code> option to Percolator and
added <code>top-match-in</code>, <code>train-best-positive</code> and
<code>spectral-counting-fdr</code> options.</li>
<li>
Improved handling of the istopic-mass parameter in
search-for-xlinks.</li>
<li>
Allow amino acids J (leucine or isoleucine), O (pyrrolysine, and U
(selenocysteine) with the <code>tide-index</code> command.</li>
<li>
Added target/decoy column to tide-search and search-for-xlinks
output files.</li>
<li>
Fixed mstoolkit to allow building with more recent versions of
GCC.</li>
<li>
Fixed bug in tide-search that used total candidate count in
output, rather than target candidate count.</li>
<li>
Fixed the percolator picked-protein option.</li>
<li>
Fixed error in handling of the custom-enzyme option.</li>
<li>
Fixed subtract-index so that it performs the subtraction only on the target
peptides, and then removes for each subtracted target its corresponding
decoy. Previously, the command did a simple subtraction separately on the
targets and on the decoys.</li>
<li>
Fixed error that caused subtract-index to ignore the mass-precision
option.</li>
<li>
Fixed error in search-for-xlinks that allowed too many missed
cleavages.</li>
<li>
Fixed error in search-for-xlinks related to average mass.</li>
<li>
Fix an error in the processing of the peptide-list option to
subtract-index.</li>
<li>
Fixed error in search-for-xlinks that attempted to use reversed decoys.
search-for-xlinks only supports shuffled decoys.</li>
<li>
Numerous minor bug fixes and improvements to the documentation.</li>
<li>
Added 'How can I search my isotopically labeled data with Tide or
Comet' to the FAQ.</li>
<li>
Added 'How do Tide and Comet handle combinations of static and variable
modifications, as well as n-terminal modifications?' to the FAQ.</li>
<li>
Updated tutorial for test-fdr in percolator.</li>
<li>
Fixed a bug with target-decoy competition in assign-confidence when multiple
matches had the same score.</li>
</ul>
<hr/>
<h3>Version 3.1</h3> January 10, 2017
<h4>Major changes</h4>
<ul>
<li>Updated Crux to always use the latest version of Percolator on
GitHub, rather than the most recent tagged release.</li>
<li>Added the Param-medic command to perform automated inference of
precursor and fragment m/z parameters. Param-medic options are
also available for Comet and Tide.</li>
<li>Added the isotope-error parameter to Tide.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
Added support for several new options to Percolator (search-input,
tdc, subset-max-train).</li>
<li>
Allow assign-confidence to rank by Percolator score.</li>
<li>
Added +1 to the numerator of the FDR estimation when
carrying out target-decoy competition. This correction was
proposed by Barber and
Candes, <a href="https://arxiv.org/abs/1404.5609"><i>Annals of
Statistics</i></a>, 2015, as well as by He et al.,
<a href="http://arxiv.org/abs/1501.00537"</a>arXiv:1501.00537</a>,
2015.</li>
<li>
Fixed incorrect default value for the cpos parameter to
percolator.</li>
<li>Many other minor bug fixes and enhancements.</li>
</ul>
<hr/>
<h3>Version 3.0</h3> August 1, 2016
<h4>Major changes</h4>
<ul>
<li>
The <code>tide-search</code> command now supports threading. See the
<code>num-threads</code> parameter for details.</li>
<li>
Added the <code>pipeline</code> command to run a series of commands, and
the <code>cascade-search</code> to run searches across a series of
databases.</li>
<li>
Renamed the command <code>calibrate-scores</code>
to <code>assign-confidence</code> and completely revamped its
functionality.</li>
<li>
The <code>search-for-xlinks</code> command offers parameters to
control categories of
candidates: <code>xlink-include-inter</code>, <code>xlink-include-intra</code>,
and
<code>xlink-include-inter-intra</code>.</li>
<li>
Added the <code>peptide-centric-search</code> option to tide-search.</li>
<li>
Compiling the Mac OS version now requires OS X Yosemite. It can be built
from source using the Clang compilers distributed with the latest version of
XCode.</li>
<li>
32-bit and 64-bit Windows versions are now available, built using Visual Studio 2013.</li>
<li>
Updated Percolator to version 2.10.</li>
<li>
Updated Hardklor to version 2.30.</li>
<li>
Updated Comet to version 2016.01 rev. 1.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
The Windows version of Crux can be built with support for vendor specific file
formats disabled.</li>
<li>
Added the <code>temp-dir</code> option
to <code>tide-index</code>.</li>
<li>
The utilities <code>create-docs</code>, <code>subtract-index</code>,
and <code>psm-convert</code> were added to Crux.</li>
<li>The <code>generate-peptides</code> application has been revamped.</li>
<li>Fixed a bug in <code>barista</code> that occurred when the number of
peptides exceeded the number of PSMs.</li>
<li>Precursor mass selection is fixed in <code>tide-search</code> when units
are m/z.</li>
<li><code>hardklor</code> and <code>bullseye</code> now use standard logging.</li>
<li>Version number added to log files. Additionally, the version numbers of
<code>percolator</code>, <code>comet</code>, and <code>boost</code> are shown
in the output of the <code>version</code> command.</li>
<li>
Short usage message is displayed on error (the full usage message is still
displayed when a command is entered with no arguments).</li>
<li>
<code>feature-in-file</code> parameter added to <code>percolator</code>.</li>
<li>
The <code>seed</code> parameter for <code>percolator</code> has been renamed
to <code>percolator-seed</code>.</li>
<li>
<code>comet</code> exits with return code 1 on failure, rather than 0.</li>
<li>
Default value for <code>use_sparse_matrix</code> changed to <code>1</code>.</li>
<li>
Default value for <code>use-neutral-loss-peaks</code> changed to <code>true</code>.</li>
<li>
<code>xlink-score-method</code> parameter added to <code>xlink-score-spectrum</code>.</li>
<li>
deltaLCn column added to <code>tide-search</code> tab-delimited output.</li>
<li>
Bug fixed in reporting flanking amino acids in <code>PostProcessProtein.cpp</code>.</li>
<li>
<code>Mix-max</code> procedure is updated to handle ties among target and decoy scores.</li>
<li>
Default value of <code>use-neutral-loss-peaks</code> changed to <code>true</code></li>
<li>
<code>Exact p-value</code> calculation takes into account the flanking and neutral loss peaks. </li>
<li>
A bug was fixed in the naming of the Percolator input (.pin) file that
is produced by Comet when the <code>output_percolatorfile</code>
option is turned on. Previously, the file was named "comet.tsv"; now
it is "comet.target.pin."</li>
<li>
<code>Assign-confidence</code> can take multiple input files.
</li>
<li>
The <code>comet</code> command can take multiple input files.
</li>
<li>
The <code>sidak</code> option has been added
to <code>assign-confidence</code> to perform a Sidak adjustment.
</li>
<li>
The <code>peptide-level</code> option has been added
to <code>assign-confidence</code>.
</li>
<li>
The refactored XCorr score has been re-scaled (by dividing by 20) to
put it into a range that is comparable to that of the original XCorr score.</li>
<li>
The default value of <code>mz-bin-offset</code> has been changed from
0.68 to 0.40.</li>
<li>
The <code>percolator</code> command outputs the <code>pout</code> XML format
again (controlled by the <code>pout-output</code> parameter).</li>
<li>
The <code>percolator</code> command can output its native output by using the
<code>original-output</code> parameter.</li>
<li>
Fixed a bug in <code>tide-search</code> causing it to fail when
<code>remove-precursor-peak</code> removed all peaks in a spectrum.</li>
<li>
The <code>max-precursor-charge</code> parameter
for <code>tide-search</code> has been introduced.</li>
<li>
Fixed a bug in candidate peptide selection when m/z tolerance is
used.</li>
<li>
Added the <code>read-tide-index</code> command, which reads an index produced
by <code>tide-index</code> and prints a list of peptides it contains.</li>
<li>
Added the <code>stop-after</code> option to print-processed-spectra, which
controls the point at which to stop preprocessing.</li>
<li>
The <code>tide-search</code> command now accepts multiple spectrum input files.
</li>
<li>
Added the <code>use-z-line</code> option to specify whether precursor
information is taken from the S or Z line when parsing MS2 files using
ProteoWizard.</li>
<li>
Added missing options to the <code>percolator</code> command.</li>
<li>
The <code>tide-search</code> command may now accept a FASTA database in
place of the index, in which case <code>tide-index</code> will be run prior to
the search. The <code>store-index</code> option allows the generated index
to be saved.</li>
<li>
The <code>assign-confidence</code> command will automatically detect
score type if the <code>score</code> parameter is not specified, searching for
xcorr, e-value, or exact p-values.</li>
<li>
The <code>cascade-search</code> will report the source index database of the
peptide for all identified PSMs.</li>
<li>
The <code>top-match</code> parameter has been removed from
<code>cascade-search</code>.</li>
<li>
<code>Assign-confidence</code> has got new options: "combine-modified-peptide"
and "combine-charge-states".</li>
<li>
<code>Assign-confidence</code> now supports top-match>1 in peptide-level filtering
mode.</li>
<li>
<code>Assign-confidence</code> can use smoothed-p-value scores for PSM ranking.</li>
<li>
<code>Assign-confidence</code> now does not carry out target-decoy competition in
peptide-level filtering mode.</li>
<li>
Added the <code>xlink-assign-ions</code> and <code>xlink-score-spectrum
</code> commands.</li>
<li>
Rearranged estimation methods in <code>assign-confidence</code>.</li>
<li>
Added top-match option for <code>estimation-method=peptide-level</code>
case in <code>assign-confidence</code>.</li>
<li>
Modified assign-confidence so that ties during target-decoy
competition are broken randomly.</li>
<li>
Changed the Percolator output feature "file" to contain the name of
the file containing the spectrum (if available), rather than the
name of the file containing the PSM.</li>
<li>
Added to <code>search-for-xlinks</code>, <code>xlink-assign-ions</code>
and <code>xlink-score-spectrum</code> parameters of the form
"use-a-ion" for a, b, c, x, y, and z-ions.</li>
<li>Various other minor bug/leak fixes and performance enhancements.</li>
<li>Added the <code>allow-dups</code> option to tide-index.</li>
</ul>
<hr></hr>
<h3>Version 2.1</h3> October 8, 2014
<h4>Major enhancements</h4>
<ul>
<li>
The <code>tide-search</code> command now supports calculation of exact
p-values via dynamic programming, as described
in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this
article</a>. The p-value calculation is controlled with
the <code>exact-p-value</code> parameter.</li>
<li>
<code>search-for-xlinks</code> now supports variable modifications and
larger protein databases. This new code is disabled by default, but
can be turned on by setting the
parameter <code>use-old-xlink=F</code>.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
The default value of <code>mz_bin_offset</code> has been changed to 0.40 from 0.68.</li>
<li>
The <code>centroided</code> parameter for the <code>hardklor</code> command is
now implemented.</li>
<li>
The <code>spectrum-format</code> parameter for the <code>bullseye</code> command
works properly.</li>
<li>
The <code>tide-search</code> command now uses information from the Z line rather
than the S line when reading spectrum files in the MS2 file format.</li>
<li>
The <code>tide-search</code> command now accepts the
<code>spectrum-parser</code> parameter.</li>
<li>
The <code>protein-database</code> parameter
to <code>spectral-counts</code> now only accepts fasta files. Parsing
of a protein index is no longer supported.</li>
<li>
A bug was fixed in the <code>spectral-counts</code> command that prevented
<code>tide-search</code> output files from being parsed correctly.</li>
<li>
The <code>default-direction</code> parameter now takes a string value of the feature
name rather than an integer.
</li>
<li>
The parameters <code>mz-bin-width</code> and <code>mz-bin-offset</code> have been added
to <code>tide-search</code>.</li>
<li>
Percolator output now includes, for each PSM, the name of the file
in which the spectrum resides.
</li>
<li>
The parameters <code>clip-nterm-methionine</code>, <code>keep-terminal-aminos</code>, and <code>min-mods</code> have been added to <code>tide-index</code>.
</li>
<li>
The parameters <code>use-flanking-peaks</code>
and <code>use-neutral-loss-peaks</code> have been added to
<code>tide-search</code>.</li>
<li>
The calculation of XCorr was simplified in Tide. In the new version,
<code>tide-index</code> only generates peptides and sorts them,
leaving the generation of theoretical peaks to be done entirely on the
fly by <code>tide-search</code>.</li>
<li>
The <code>tide-search</code> command now prints search progress reports both to
the screen and to the log file. The interval at which progress is printed can
be controlled using the <code>print-search-progress</code> parameter.</li>
<li>
The <code>calibrate-scores</code> command now outputs files with the stem
"calibrate-scores" rather than "qvalue."</li>
<li>
The <code>use-flanking-peaks</code> parameter now has a default value of
false.</li>
<li>
The Comet search engine was updated to version 2014011.</li>
<li>
The MSToolkit parser was updated to the latest version (r73).</li>
<li>
The <code>version</code> command now outputs the revision number.</code>
<li>
Various improvements in performance and error handling were implemented.</li>
</ul>
<hr></hr>
<h3>Version 2.0</h3> June 6, 2014
<h4>Major enhancements</h4>
<ul>
<li>
Two new search engines are now included in Crux: Comet and Tide. The
old search engine, search-for-matches, has been retired.</li>
<li>Percolator has been updated to version 2.07.</li>
<li>
Crux now compiles in native Windows, rather than requiring
Cygwin. Consequently, Crux running under Windows can parse vendor
proprietary formats using the appropriate Proteowizard libraries.</li>
</ul>
<h4>Minor changes</h4>
<ul>
<li>
The "enyzme" parameters "lysc", "lysn", "arg_c", "glue_c", and
"pepsin_a" were renamed to "lys-c", "lys-n", "arg-c", "glue-c", and
"pepsin-a".</li>
<li>
Percolator outputs decoy files in addition to target files.</li>
<li>
Percolator tab-delimited peptides output now contain a posterior error
probability (PEP) column.</li>