Release notes for Crux
Minor changes
- 25 July 2023: crux percolator --pepxml-output T now uses internal percolator code to generate pepxml output.
- 10 July 2023: Added support for the percolator --no-terminate option, which allows execution to continue even if the SVM encounters issues.
- 30 May 2023: File overwrite bug fix in diameter
- 14 April 2023: Added by-ions matched, by-ions total, and by-ions-fraction columns to tide-search output in case of standard XCorr scoring.
- 14 March 2023: Added a new column, called "unmodified sequence," to tab-delimited outputs. This column contain the peptide sequence without modifications. The new column appears in tide-search, diameter, assign-confidence, and cascade-search results.
- 14 March 2023: The "cleavage type" column was removed from tab-delimited outputs produced by tide-search, diameter, and assign-confidence.
- 20 Feb 2023: Tide-index aux locations were merged into the peptide protocol buffer.
- 20 Feb 2023: Tide-index now shuffles modified and unmodified target peptides in the same way.
- 19 Feb 2023: Add a "filename" column to the Percolator tab-delimited output files.
- 07 Feb 2023: Fix bug in mix-max procedure. The q-values are now the smallest FDRs for the associated thresholds.
- 13 Jan 2023: Tide-search halts with an error message when the user tries to use tailor-calibration in conjunction with peptide-centric search.
- 13 Jan 2023: Added a check to verify that these release notes are updated in every pull request.
- 09 Jan 2023: Upgraded to Comet 2022.01 rev 2. Fixed issue #572: handling of Comet isotope_error option (now allows values 0-5).
- 04 Jan 2023: Fix divide-by-zero bug in postprocessing diameter results.
- 16 Dec 2022: Changed the default precision for specifying variable modifications to four decimal points rather than two.
- 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.
- 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.
- 28 Sept 2022: Updated Assign-confidence to the new comet output.
- 28 Sept 2022: Updated performance and smoke tests
- 28 Sept 2022: Added option to tide-search to search spectra in a min- and max-precursor-charge range.
- 28 Sept 2022: Removed the option from tide-index to generate decoy protein fasta file.
- 28 Sept 2022: Fixed bug in tide index which prevented it generating terminal variable modifications.
- 28 Sept 2022: Fixed bug in tide index which slowed it down when generating many mods.
- 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.
- 17 August 2022: Updated to percolator committ 1e82daa.
- 27 July 2022: Fixed bug preventing percolator from running on Kojak output.
- 19 July 2022: Added min_peptide_score parameter to Kojak.
- 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.
- Upgraded to Protocol Buffers 3.19.4
- Upgraded to GFlags 2.2.2
- 09 June 2022: Added support for building using GitHub Actions.
- 01 May 2022: XCorr scoring implementing in C++. This resolves a longstanding bug in our multithreading code.
- 20 Jan 2022: The XCorr scoring, exact p-value, and ResEv in Tide-Search has been sped up.
- 10 Jan 2022: Fixed bug that resulted in rank=0 for search results in pepxml files (issue #521).
- 16 Nov 2021: The preprocessing of the exact p-value method has been aligned to the preprocessing of the standard XCorr scoring.
- 16 Nov 2021: Comet has been upgraded to version 2021.01.0.
- 16 Nov 2021: Kojak has been upgraded to commit defa8c9.
- 16 Nov 2021: MSToolkit has been upgraded to commit 4cb705d.
- 16 Nov 2021: IUPAC symbol 'O' is now the amino acid pyrrolysine.
- 16 Nov 2021: Dropped support for 32-bit versions of Crux.
- 9 Nov 2021: Fix the crash bug in
diameter
when there is no MS1 spectrum in the input file. - 5 Nov 2021: Update the param-medic documentation to include pointers to published papers and to describe detection of modifications.
- 30 Oct 2021: Remove the protein-reverse option from "--decoy-format" in
tide-index
andgenerate-peptides
. - 23 Oct 2021: Revised the
tide-index
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. - 18 Oct 2021: Fixed a bug in DIAmeter that caused it to detect 0 PSMs when the
windowWideness
property is missing in the input file. - 18 Oct 2021: Revised the DIAmeter documentation to clarify which options are affected by the setting of
diameter-instrument
.
Version 4.1
October Oct. 11, 2021Major changes
- 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
Lu et al. Bioinformatics 37(Supplement_1):i434–i442, 2021.
Minor changes
- 14 Sept 2021: Add second set of smoke-tests that give tide-search a FASTA file instead of a database index.
- 14 Sept 2021: Replace contents of demo.ms2 in the tutorials with new data (bug #454).
- 10 Jun 2021: Fixed bug in computing the m/z window size in
Tide. Affected only the setting when
precursor-window-type=mz
. - 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.
- 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.
- 11 May 2021: Added smoke tests to test case where tide-search is given a FASTA file instead of a index.
Version 4.0
April 06, 2021Major changes
- 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.
- Nov. 6, 2020: Updated to use Comet 2019.05.
- Nov. 6, 2020: Added Kojak module for searching for cross-linked peptides.
The methodology is described in
Hoopmann et al. Journal of Proteome Research, 2015.
- July 23, 2019: Added the Tailor PSM score calibration method to Tide-search as
an option.
- 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.
-
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
May
et al. Journal of Proteome Research, 2019.
Minor changes
-
Mar 10, 2021: Changed num-threads default to 1.
-
Feb. 12, 2021: Added date of latest commit to version string.
-
Feb. 11, 2021: Fixed bug in support for comet. Output files were
being stored in the wrong directory when multiple spectra files
were provided.
-
Feb 9, 2021: Added process ID number to the names of temporary
files created by Tide, to avoid conflicts.
-
Jan. 11, 2021: Fixed break in build of Percolator.
-
December 7, 2020: Updated documentation to remove "+" from the usage statement.
-
December 4, 2020: Updated schematic diagram of Crux tools.
-
December 3, 2020: Fixed bug in peptide-centric search that caused
mis-scaling of XCORR score on some Linux systems.
-
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"
-
Sept. 18, 2020: Updated MGF file parser to handle title line.
-
August 28, 2020: Updated documentation for --use-neutral-loss-peaks.
-
August 27, 2020: Added support for protein terminal modifications. See FAQ page for details.
-
August 7, 2020: Added --lysarginase as an enzyme option to tide-index
and generate-peptides. The rule this enzyme follows is [ ]:[KR].
-
May 28, 2020: Added fixes for pepXML schema validation failures.
-
April 28, 2020: Added the --brief-output option to tide-search,
which prints only a subset of fields to the output file.
-
April 27, 2020: Fixed build of Percolator to use BLAS libraries.
-
March 18, 2020: Crux now builds MSTookit from original repository
rather than a fork.
-
December 16, 2019: Fixed a bug in Tailor method where minimal number of candidate
peptides were selected incorrectly.
-
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.
-
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.
-
October 1, 2019: Added the "--static" option for percolator to enable the
use of pretrained, static models.
-
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.
-
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.
-
April 16, 20219: Fixed Windows path parsing bug in spectral-counts.
-
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.
-
November 6, 2018: Decoy generation will now allow duplicate decoy peptides
within a decoy database and bewteen decoy databases.
-
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.
-
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.
-
August 22, 2018: Fixed a bug causing filenames to be blank in
Percolator outputs.
-
August 14, 2018: Improved handling for terminal modifications when
parsing peptide sequences.
-
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.
-
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.
-
June 19, 2018: Updated comet to release 2018012.
-
May 30, 2018: Fixed a bug in spectral-counts that affected how the
parsimony flag reported peptide ranks.
Version 3.2.x
June 19, 2018
Major changes
-
Crux on Linux now requires v 2.17 or higher of the C runtime libraries.
- Building Crux on Windows now requires Visual Studio 2017
Minor changes
- Fixed documentation errata
- Disabled network access by Comet
- Updated to Comet 2018012
- A 32-bit Linux version of Crux can be built on 64-bit Linux machines.
- Added support for parsing UNIMOD modifications.
Version 3.2
May 20, 2018
Major changes
-
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
"Combining
high resolution and exact calibration to boost statistical power: A
well-calibrated score function for high-resolution MS2
data".
-
Implemented the "average target-decoy competition" protocol
in
assign-confidence
. More details are available in
"Progressive
calibration and averaging for tandem mass spectrometry statistical
confidence estimation: Why settle for a single decoy?".
-
Added the localize-modification command to find the most likely locations
of post-translational modifications on peptides from a set of
peptide-spectrum matches.
-
Improved handling of modifications in tide-index, allowing for indices
containing many different types of modifications.
Minor changes
-
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.
-
Percolator and make-pin can now accept multiple files on the
command line.
-
Updated Comet to version 2018.01 rev. 0.
-
Implemented improvements to I/O speed for MzIdent format.
-
Crux distributions are now identified using an abbreviated unique
string from the version control system.
-
Added support for mzML to qranker and barista.
-
Modified tide-search to reports peak counts separately for each
thread.
-
Added "deisotope" option to tide-search.
-
Added "max-charge-feature" option to make-pin so
that the user can control how many charge features are
created.
-
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.
-
Added the "mod-precision" option to control the
number of digits used to represent post-translational
modifications in various output files.
-
Modified cascade-search so that the q-value threshold is not
applied to the final database in the cascade.
-
Tide-index will now clip methionines at the begining of proteins that do
not have an internal clevage site.
-
Enabled search-for-xlinks to search multiple spectra files,
in any of the file formats supported by Proteowizard. Support for the
file-column
option added.
-
Added the print-progress, concat, and mono-link options to
search-for-xlinks and simplified the mod option.
-
Changed the tide-search precursor-window option upper bound from
100 to 1,000,000,000 to allow open modification searching.
-
Added PepXML support for mod_nterm_mass and mod_cterm_mass on
modification_info.
-
Removed the
feature-file-in
option to Percolator and
added top-match-in
, train-best-positive
and
spectral-counting-fdr
options.
-
Improved handling of the istopic-mass parameter in
search-for-xlinks.
-
Allow amino acids J (leucine or isoleucine), O (pyrrolysine, and U
(selenocysteine) with the
tide-index
command.
-
Added target/decoy column to tide-search and search-for-xlinks
output files.
-
Fixed mstoolkit to allow building with more recent versions of
GCC.
-
Fixed bug in tide-search that used total candidate count in
output, rather than target candidate count.
-
Fixed the percolator picked-protein option.
-
Fixed error in handling of the custom-enzyme option.
-
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.
-
Fixed error that caused subtract-index to ignore the mass-precision
option.
-
Fixed error in search-for-xlinks that allowed too many missed
cleavages.
-
Fixed error in search-for-xlinks related to average mass.
-
Fix an error in the processing of the peptide-list option to
subtract-index.
-
Fixed error in search-for-xlinks that attempted to use reversed decoys.
search-for-xlinks only supports shuffled decoys.
-
Numerous minor bug fixes and improvements to the documentation.
-
Added 'How can I search my isotopically labeled data with Tide or
Comet' to the FAQ.
-
Added 'How do Tide and Comet handle combinations of static and variable
modifications, as well as n-terminal modifications?' to the FAQ.
-
Updated tutorial for test-fdr in percolator.
-
Fixed a bug with target-decoy competition in assign-confidence when multiple
matches had the same score.
Version 3.1
January 10, 2017
Major changes
- Updated Crux to always use the latest version of Percolator on
GitHub, rather than the most recent tagged release.
- 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.
- Added the isotope-error parameter to Tide.
Minor changes
-
Added support for several new options to Percolator (search-input,
tdc, subset-max-train).
-
Allow assign-confidence to rank by Percolator score.
-
Added +1 to the numerator of the FDR estimation when
carrying out target-decoy competition. This correction was
proposed by Barber and
Candes, Annals of
Statistics, 2015, as well as by He et al.,
arXiv:1501.00537,
2015.
-
Fixed incorrect default value for the cpos parameter to
percolator.
- Many other minor bug fixes and enhancements.
Version 3.0
August 1, 2016
Major changes
-
The
tide-search
command now supports threading. See the
num-threads
parameter for details.
-
Added the
pipeline
command to run a series of commands, and
the cascade-search
to run searches across a series of
databases.
-
Renamed the command
calibrate-scores
to assign-confidence
and completely revamped its
functionality.
-
The
search-for-xlinks
command offers parameters to
control categories of
candidates: xlink-include-inter
, xlink-include-intra
,
and
xlink-include-inter-intra
.
-
Added the
peptide-centric-search
option to tide-search.
-
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.
-
32-bit and 64-bit Windows versions are now available, built using Visual Studio 2013.
-
Updated Percolator to version 2.10.
-
Updated Hardklor to version 2.30.
-
Updated Comet to version 2016.01 rev. 1.
Minor changes
-
The Windows version of Crux can be built with support for vendor specific file
formats disabled.
-
Added the
temp-dir
option
to tide-index
.
-
The utilities
create-docs
, subtract-index
,
and psm-convert
were added to Crux.
- The
generate-peptides
application has been revamped.
- Fixed a bug in
barista
that occurred when the number of
peptides exceeded the number of PSMs.
- Precursor mass selection is fixed in
tide-search
when units
are m/z.
hardklor
and bullseye
now use standard logging.
- Version number added to log files. Additionally, the version numbers of
percolator
, comet
, and boost
are shown
in the output of the version
command.
-
Short usage message is displayed on error (the full usage message is still
displayed when a command is entered with no arguments).
-
feature-in-file
parameter added to percolator
.
-
The
seed
parameter for percolator
has been renamed
to percolator-seed
.
-
comet
exits with return code 1 on failure, rather than 0.
-
Default value for
use_sparse_matrix
changed to 1
.
-
Default value for
use-neutral-loss-peaks
changed to true
.
-
xlink-score-method
parameter added to xlink-score-spectrum
.
-
deltaLCn column added to
tide-search
tab-delimited output.
-
Bug fixed in reporting flanking amino acids in
PostProcessProtein.cpp
.
-
Mix-max
procedure is updated to handle ties among target and decoy scores.
-
Default value of
use-neutral-loss-peaks
changed to true
-
Exact p-value
calculation takes into account the flanking and neutral loss peaks.
-
A bug was fixed in the naming of the Percolator input (.pin) file that
is produced by Comet when the
output_percolatorfile
option is turned on. Previously, the file was named "comet.tsv"; now
it is "comet.target.pin."
-
Assign-confidence
can take multiple input files.
-
The
comet
command can take multiple input files.
-
The
sidak
option has been added
to assign-confidence
to perform a Sidak adjustment.
-
The
peptide-level
option has been added
to assign-confidence
.
-
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.
-
The default value of
mz-bin-offset
has been changed from
0.68 to 0.40.
-
The
percolator
command outputs the pout
XML format
again (controlled by the pout-output
parameter).
-
The
percolator
command can output its native output by using the
original-output
parameter.
-
Fixed a bug in
tide-search
causing it to fail when
remove-precursor-peak
removed all peaks in a spectrum.
-
The
max-precursor-charge
parameter
for tide-search
has been introduced.
-
Fixed a bug in candidate peptide selection when m/z tolerance is
used.
-
Added the
read-tide-index
command, which reads an index produced
by tide-index
and prints a list of peptides it contains.
-
Added the
stop-after
option to print-processed-spectra, which
controls the point at which to stop preprocessing.
-
The
tide-search
command now accepts multiple spectrum input files.
-
Added the
use-z-line
option to specify whether precursor
information is taken from the S or Z line when parsing MS2 files using
ProteoWizard.
-
Added missing options to the
percolator
command.
-
The
tide-search
command may now accept a FASTA database in
place of the index, in which case tide-index
will be run prior to
the search. The store-index
option allows the generated index
to be saved.
-
The
assign-confidence
command will automatically detect
score type if the score
parameter is not specified, searching for
xcorr, e-value, or exact p-values.
-
The
cascade-search
will report the source index database of the
peptide for all identified PSMs.
-
The
top-match
parameter has been removed from
cascade-search
.
-
Assign-confidence
has got new options: "combine-modified-peptide"
and "combine-charge-states".
-
Assign-confidence
now supports top-match>1 in peptide-level filtering
mode.
-
Assign-confidence
can use smoothed-p-value scores for PSM ranking.
-
Assign-confidence
now does not carry out target-decoy competition in
peptide-level filtering mode.
-
Added the
xlink-assign-ions
and xlink-score-spectrum
commands.
-
Rearranged estimation methods in
assign-confidence
.
-
Added top-match option for
estimation-method=peptide-level
case in assign-confidence
.
-
Modified assign-confidence so that ties during target-decoy
competition are broken randomly.
-
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.
-
Added to
search-for-xlinks
, xlink-assign-ions
and xlink-score-spectrum
parameters of the form
"use-a-ion" for a, b, c, x, y, and z-ions.
- Various other minor bug/leak fixes and performance enhancements.
- Added the
allow-dups
option to tide-index.
Version 2.1
October 8, 2014
Major enhancements
-
The
tide-search
command now supports calculation of exact
p-values via dynamic programming, as described
in this
article. The p-value calculation is controlled with
the exact-p-value
parameter.
-
search-for-xlinks
now supports variable modifications and
larger protein databases. This new code is disabled by default, but
can be turned on by setting the
parameter use-old-xlink=F
.
Minor changes
-
The default value of
mz_bin_offset
has been changed to 0.40 from 0.68.
-
The
centroided
parameter for the hardklor
command is
now implemented.
-
The
spectrum-format
parameter for the bullseye
command
works properly.
-
The
tide-search
command now uses information from the Z line rather
than the S line when reading spectrum files in the MS2 file format.
-
The
tide-search
command now accepts the
spectrum-parser
parameter.
-
The
protein-database
parameter
to spectral-counts
now only accepts fasta files. Parsing
of a protein index is no longer supported.
-
A bug was fixed in the
spectral-counts
command that prevented
tide-search
output files from being parsed correctly.
-
The
default-direction
parameter now takes a string value of the feature
name rather than an integer.
-
The parameters
mz-bin-width
and mz-bin-offset
have been added
to tide-search
.
-
Percolator output now includes, for each PSM, the name of the file
in which the spectrum resides.
-
The parameters
clip-nterm-methionine
, keep-terminal-aminos
, and min-mods
have been added to tide-index
.
-
The parameters
use-flanking-peaks
and use-neutral-loss-peaks
have been added to
tide-search
.
-
The calculation of XCorr was simplified in Tide. In the new version,
tide-index
only generates peptides and sorts them,
leaving the generation of theoretical peaks to be done entirely on the
fly by tide-search
.
-
The
tide-search
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 print-search-progress
parameter.
-
The
calibrate-scores
command now outputs files with the stem
"calibrate-scores" rather than "qvalue."
-
The
use-flanking-peaks
parameter now has a default value of
false.
-
The Comet search engine was updated to version 2014011.
-
The MSToolkit parser was updated to the latest version (r73).
-
The
version
command now outputs the revision number.
-
Various improvements in performance and error handling were implemented.
Version 2.0
June 6, 2014
Major enhancements
-
Two new search engines are now included in Crux: Comet and Tide. The
old search engine, search-for-matches, has been retired.
- Percolator has been updated to version 2.07.
-
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.
Minor changes
-
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".
-
Percolator outputs decoy files in addition to target files.
-
Percolator tab-delimited peptides output now contain a posterior error
probability (PEP) column.
-
The Percolator tab-delimited peptide output has been corrected to show
the PSM with the best score, rather than the worst.
-
The Percolator tab-delimited PSMs output "matches/spectrum" value has
been corrected.
-
A new utility command,
make-pin
, is provided to create
input files for use by Percolator.
-
The
spectrum-min-mass
and spectrum-max-mass
options have been renamed to spectrum-min-mz
and
spectrum-max-mz
, respectively.
-
A
spectrum-parser
option was added to q-ranker
and
barista
.
-
A bug was fixed in
q-ranker
and barista
when
reading peptides with modifications.
-
Fixed the
q-ranker
tab delimited output so that, for a
given peptide, flanking amino acids are reported for each protein that
contains that peptide, rather than only reporting one set of flanking
amino acids.
-
A bug was fixed in
percolator
, wherein the first and last
two characters were being truncated from peptide sequences when the
input was missing the flanking amino acids or when the charge state
was not indicated in the PSM IDs.
-
The crux spectrum parser has been removed.
-
Q-ranker now outputs decoy files.
-
The Boost.Random library is now being used for random number
generation.
-
calibrate-scores
no longer requires a protein input.
-
calibrate-scores
now only takes the top match per
spectrum and charge.
-
get-ms2-spectrum
now prints z-lines with Bullseye
files.
-
Various performance and error handling improvements.
Version 1.40
May 22, 2013
Major enchancements
-
Crux Percolator was updated from version 1.05 to the latest release,
version 2.04.
Minor changes
-
The formula that is used to convert fragment m/z values from real
numbers into integers was modified. Previously, the conversion was
floor( (x / mz-bin-size) + 0.5 + mz-bin-offset )
The new conversion formula is
floor( (x / mz-bin-size) + 1.0 - mz-bin-offset )
The default values of the two parameters (mz-bin-size and
mz-bin-offset) have not changed. The allowed range of the
mz-bin-offset parameter was previously [-1,1], but has been changed to
[0,1].
To understand the motivation for the changed formula, note that the
mz-bin-offset parameter controls the location of bin edges, relative
to integer masses on the mass scale. In general, mz-bin-offset should
be chosen so that bin edges fall between the expected clusters of
fragment masses. For fragments with 1+ charge, masses will cluster
near integer values (after dividing by mz-bin-width), and the ideal
value of mz-bin-offset would be 0.5. For mixtures of fragments with
1+ and 2+ charges, masses will cluster near integer and half-integer
values, so mz-bin-offset near 0.25 or 0.75 would produce bin edges
that best avoid the clusters of fragment masses. The old conversion
formula did not correctly locate bin edges, given a chosen
mz-bin-offset. The new conversion formula produces a proper
translation of mz-bin-offset into bin edge locations.
-
The
seed
parameter is now available to control the
seeding of random number generator. The default value is 1.
seed
is available as a parameter from all applications.
It can be set as a command line option for
crux search-for-matches
and
crux percolator
.
-
The default value of the
decoys
parameter for crux
search-for-matches
was incorrectly documented. The default is
actually peptide-shuffle
, but the documentation said the
default was protein-shuffle
. The documentation has been
corrected.
-
The incorrectly labeled column header
xcorr rank
in barista and
q-ranker feature files has been corrected to xcorr score
.
-
The q-ranker output file
qranker_output.xml
has been renamed to
qranker.xml
.
-
The deltaCn computation has been modified to be consistent with
Percolator. Rather than using
deltaCni = (xcorr1 - xcorri+1) / xcorr1
it is now computed using
deltaCni = (xcorri - xcorri+1) / max(xcorri, 1.0)
-
Percolator now accepts inputs in SQT, PepXML, and tab-delimited formats in addition to
the PinXML format.
-
Flags were added to several commands allowing the user to control
whether various results files are created in the output directory:
--sqt-output <T|F>
(search-for-matches)
--mzid-output <T|F>
(search-for-matches, percolator)
--pinxml-output <T|F>
(search-for-matches)
--pepxml-output <T|F>
(search-for-matches, q-ranker, barista, percolator)
--txt-output <T|F>
(search-for-matches, q-ranker, barista, percolator)
By default, all of these flags are set to false except txt-output
.
Version 1.39
October 6, 2012
Major enchancements
-
Crux is now released under an Apache license for all users.
-
Parsing MS/MS spectra is now supported using Proteowizard (v. 3.0.3950).
This allows Crux to
handle MS/MS spectra in mzML (1.0 and 1.1), mzXML, MGF, MS2 and CMS2
formats.
Use
spectrum-parser=pwiz
to enable Proteowizard parsing.
-
Crux now uses
cmake
for the build process rather than
autoconf
/automake
.
Minor changes
-
The Tide database search software is no longer distributed as part of Crux because its license is not compatible with the new Crux license.
-
Support for PIN XML output was added to
crux
search-for-matches
.
-
Fixed a bug in
crux create-index
on Windows and Cygin
that caused the program to fail with the message:
WARNING: Cannot rename directory
FATAL: Failed to create index
-
The parameter
protein database
is now an option rather than a required argument for crux spectral-counts
.
-
mzIdentML file support has been added for
crux spectral-counts
.
-
PepXML file support has been fixed for
crux spectral-counts
.
-
Fixed bug in packedNorm() that sometimes generated incorrect values for the posterior error probability.
-
Fixed bug in
crux create-index
on Windows and Cygwin that caused it to fail on Windows and Cygin.
Version 1.38
July 20, 2012
Major enhancements
-
Hardklor and Bullseye, tools for analyzing high-resolution precursor
spectra, are now incorporated into Crux.
-
Barista has been modified extensively so that it more closely
resembles the other tools in Crux:
-
Barista and Q-ranker accept search results in tab-delimited format, in addition to
SQT format.
-
Barista now reports posterior error probabilities, in addition to
q-values, for PSMs, peptides and proteins.
-
Barista's pep.xml output has been updated to be compatible with the
TransProteomic Pipeline (TPP).
-
The
sequest-search
command has been removed. The
functionality of this command is still available using options for
the search-for-matches
command (see
the frequently asked questions list for
details).
Minor changes
-
crux predict-peptide-ions
calculates the mass shift
resulting from the nh3 or h2o neutral loss correctly. Previously, a
neutral loss resulted in an addition of mass rather than subtraction.
-
crux predict-peptide-ions
reports ion-type as
'b','y','a', or 'p' rather than a number (i.e. 0, 1, 2, 3).
-
crux predict-peptide-ions
now only allows one type of
neutral loss modification per ion. Previously, multiple different
types of neutral loss could be applied simultaneously to a single
ion.
-
The
neutral-losses
option was removed from crux
predict-peptide-ions
, due to its redundancy with the supported
the --nh3
and --h2o
options.
-
crux predict-peptide-ions
supports 'bya' in the
--primary-ions
parameter, which will generate
the a-ion series in addition to the 'b' and 'y' ions.
-
The spectrum parsing is updated so that peaks with zero intensity are
ignored.
-
crux spectral-counts
now has an option to compute the raw
spectral count.
-
crux spectral-counts
now has an option to compute dNSAF
values.
-
A bug in
crux spectral-counts
was fixed so that it now
properly normalizes the NSAF value.
-
Multiple missed cleavages are now handled by
crux
search-for-xlinks
using the missed-cleavages parameter.
Previously, this was unsupported.
-
Ambiguous amino acids are handled differently. 'J' is interpreted to
indicate 'I' or 'L'. Peptides containing B, Z, and X are no longer be
allowed, and a warning is issued when these amino acid codes are
encountered.
-
The stand-alone
crux-predict-peptide-ions
and crux-generate-peptides
applications have been integrated
into the main crux
application.
-
A bug has been fixed that affected the intensity adjustment of
observed spectra when the bin width was set much larger or smaller
than 1.
-
Beginning with version 1.37, q-ranker erroneously included decoy PSMs
along with target PSMs in the q-ranker.target.psms.txt file. All PSMs
were sorted by q-ranker score so the targets and decoys were mixed
together with no accompanying labels. This bug has been fixed so that
Q-ranker once again returns only target PSMs.
-
The search option
display-summed-masses
has been replaced by
mod-mass-format
. With this option, there is a new format
for reporting modificiations: the mass in the square braces is that of the
preceeding amino acid plus the modification mass. This format is compliant
with TPP pep.xml output.
-
Modifications are reported differently in the pep.xml header to be
compliant with the TPP.
-
The command
crux compute-q-values
now reports posterior
error probabilities in addition to q-values. Consequently, the
command was renamed crux calibrate-scores
.
-
Crux now provides an explicit error message when an incorrectly
formatted MS2 file is parsed. Previously, crux simply reported that
no spectra were found.
-
Several additional scores were added to the
q-ranker
pep.xml files.
- Fixed the build procedure to work on both Lion and pre-Lion versions of OS X.
- Fixed a bug in the normalization of the observed spectra.
Previously, after the 10-bin normalization of intensities, peaks with
heights below 5% of the maximum were not being removed.
-
When a fragmentation spectra file is read, the assumed
peptide charge state information can be missing for the scans.
In cases where this information has not been provided,
Crux will now estimate the possible charge states.
-
The feature files for Q-ranker and Barista now contain a header
describing each feature.
-
Q-ranker and Barista now output all of the fields provided in the
input search files.
Version 1.37
December 22, 2011
Major enhancements
-
Added
crux barista
, a tool for inferring protein
identifications.
-
Reimplemented
crux q-ranker
with new outputs and
command-line syntax.
-
Percolator and compute-q-values now compute and report posterior error
probabilities, in addition to q-values.
-
crux create-index
now generates and store decoy
peptides in the index. Decoys can still be generated on-the-fly when
searching .fasta files.
Minor changes
-
A pair of options,
cterm-fixed
and nterm-fixed
, allow fixed terminal peptide
modifications, i.e., a mass shift applied to every peptide on either or
both termini.
-
A bug in the spectrum processing code was fixed, which was erroneously
eliminating a few of the highest m/z fragment peaks. Xcorrs have
changed slightly as a result.
-
Simplified the
--mz-bin-width
and
--mz-offset parameters so that --xcorr-var-bin
is no longer needed.
-
Indexes now store information about any static mods used when they
were created.
-
In the tab-delimited output files the 'matches/spectrum' column gives
the number of target peptides compared to the spectrum and the decoy
file has an additional column, 'decoy matches/spectrum' that gives the
number of decoy peptides compared to the spectrum. These two numbers
may differ when decoys are not generated on-the-fly.
-
The header lines of Barista and QRanker include all of the columns
in the search results.
Version 1.36
August 4, 2011
Tide changes
-
Added support for user-specifiable variable and static amino acid
modifications.
-
Tide's version of XCorr has been modified so that it is always
identical to those of a recent version SEQUEST®.
-
Added support for user-specifiable maximum number of missed enzyme
cleavage points.
-
Tide now performs basic charge state inference when this information
is missing from the spectrum input files.
-
User-specifiable output formatting, using new
the
tide-results
utility, including
- Text format with user-specifiable fields.
- SQT format.
- PepXML format.
- Choose whether to display all proteins in which each peptide occurs or
just one representative.
-
Note that new file formats are created
by
tide-index
. Index files created by previous versions
of Tide should not be used with the new version.
Minor changes
-
Q-ranker now reports q-values instead of false discovery rates.
-
Corrected several errors in the pep.xml output, related to reporting
the spectrum filename, charge, and neutral mass.
-
Changed the
missed-cleavages
option to allow specifying
the maximum number of missed cleavages in a peptide rather than
specifying none/any.
-
Fixed a bug that did not print the spectrum file name correctly in the
pep.xml files.
-
Improved the error message produced by
crux
spectral-counts
when the input PSM file does not contain the
required q-values.
-
Previously, Crux's theoretical spectrum includes two flanking peaks
around each b- and y-ion. The new
Boolean flag
use-flanking-peaks
, allows these to be
either on or off. Flanking peaks are by default in
crux sequest-search
but are not used by default
in crux search-for-matches
.
Version 1.35
March 23, 2011
Major enhancements
-
Added the
crux spectral-counts
command for estimating
protein quantification.
Minor changes
-
The spectrum neutral mass is now calculated from the m+h value
provided by the Z-lines of an MS2 file. Also, multiple z-lines of a
spectrum that have the same charge are now supported. With these
changes,
crux search-for-matches
and crux
sequest-search
can now take advantage of accurate precursor
masses in MS2 files generated by Bullseye (Hsieh et al. J. Proteome
Res. 9(2):1138-43, 2010).
-
Made the
pep.xml
file header produced by Crux compatible
with the Transproteomic Pipeline.
-
Introduced several changes to improve performance on MacOS X.
-
Added an
nterm
option to the link argument of crux
search-for-xlinks
.
Version 1.34
December 22, 2010
Minor changes
-
The default value of the "pi-zero" parameter has been changed from 0.9
to 1.0.
-
A new option
--peptide-list
has been added to crux
create-index
. When set to T, this option causes an ASCII
file of peptides to be included in the output directory. Each line
of the file lists the peptide sequence and its neutral mass.
-
The default bin offset was returned to 0.68. It had erroneously been
changed to 0 in version 1.33.
-
A new option
--compute-sp
has been added to crux
search-for-matches
. When set to true, all candidate peptides
will be scored by Sp in addition to xcorr. This option is recommended
for generating input to percolator
or q-ranker
.
-
Added
max-ion-charge
parameter to designate the maximum
charge for theoretical ions in crux search-for-xlinks
and
crux xlink-assign-ions
.
-
Modifications may optionally indicate if they prevent cleavage or
prevent cross linking.
-
Results are printed to .pep.xml files in addition to .txt files.
-
Added a
mass-precision
option which sets how many digits
are written for all mass and m/z values in .txt, .sqt, and .ms2 files.
-
The columns printed to the .txt files now vary with the
crux
command being run and the settings so that unused
columns are not printed.
-
Fixed a bug that limited what files were used as input for post-search
commands (e.g.
crux percolator
) based on fileroot. Now
files with different fileroots can be analyzed together.
-
Fixed a bug that caused searches using fasta files to search peptides
multiple times if they appeared in a file multiple times.
Version 1.33
July 7, 2010
Major enhancements
-
The command line syntax
for
compute-q-values
, percolator
and q-ranker
was modified to allow the programs to read
from and write to separate directories.
-
A bug in q-ranker and percolator was fixed. This bug was introduced
several versions ago, and it led to erroneously many PSMs receiving
very small q-values. The problem relates to the scaling of the delta
Cn feature, and the fix is a temporary stopgap: we remove the feature
entirely. The next version should have the corrected feature in
place.
Minor changes
-
A new option
--min-peaks
has been added to set a filter
for the minimum number of peaks a spectrum must have in order for it
to be searched. The default minimum is 20 peaks.
-
The hardcoded limit for the number of proteins allowed in a database
has been removed.
-
The hardcoded limit for the number of spectra and the number of
peaks/spectrum has been removed.
-
A new option
--xcorr-var-bin
has been added to toggle the
new binning of the m/z axis. The default bin offset was returned back
to 0, but the default bin width is still 1.000508. (Note: this
erroneous change was subsequently reverted in version 1.34.)
-
The option
--max-ion-charge
now places a limit on the
maximum charge state of the ions generated for the xcorr theoretical
spectra for crux search-for-xlinks
. This change is also
supported by xlink-assign-ions
.
-
The option
--no-xval
was added to q-ranker, allowing
faster execution by skipping the internal cross-validation to select
hyperparameters.
-
The precision of modification masses written to the .txt files now matches
the maximum precision given in the parameter file.
-
Sub-options
prevents cleavage
and
prevents cross-link
have been added to variable modifications
and support has been provided for the "prevents cleavage"
sub-option.
Version 1.32
July 6, 2010
Major enhancement
-
Version 1.32 includes changes only to Tide. A new binary is introduced
— a modified version of ProteoWizard's msconvert program
— that is capable of converting spectrum data from a wide range
of file formats into Tide-readable .spectrumrecords input
files.
Minor changes
-
tide-import-spectra is removed from the distribution. Although
it was faster than msconvert, it was specific to ms2 files, whereas
msconvert now works with any ProteoWizard-supported file format.
-
A standalone utility for reading binary .spectrumrecords files
is introduced, called read-spectrumrecords. This program is
useful, for example, for visually checking the output of msconvert.
-
Demo input files worm-06-10000.spectrumrecords
and yeast-02-10000.spectrumrecords now replace their
counterparts worm-06-10000.ms2 and yeast-02-10000.ms2. With the
introduction of Tide-compatible msconvert, ms2 files are in no way
special to Tide anymore. Any ProteoWizard-supported file format can be
converted to the .spectrumrecords format for use with
Tide. Starting with data files in Tide's spectrumrecords format
eliminates the conversion step in the Tide search demo.
-
The old demo scripts worm-demo.sh and yeast-demo.sh have each been
replaced by a pair of new scripts that demonstrate the indexing and
searching steps separately. This is in order to highlight the two-step
process and the fact that indexing needs to be done just once for each
fasta file, whereafter the index may be reused indefinitely to perform
searches.
Version 1.31
June 2, 2010
Major enhancements
-
This version of Crux is released with a demo version of a new search
engine, Tide. Tide is an independent
reimplementation of the SEQUEST® algorithm. The
immediate ancestor of Tide is the Crux
search-for-matches
command, but Tide has been completely re-engineered to achieve a
thousandfold improvement in speed while exactly replicating Crux XCorr
scores. Currently, Tide is not fully integrated with Crux, and is
available only in binary executable format.
Minor changes
-
Two options have been added to
crux search-for-matches
(--mz-bin-width
and --mz-bin-offset
) to
allow control of the binning of the m/z axis.
-
The
ion-tolerance
option was removed from the search
tools.
-
The default location of the left edge of the first bin along the m/z
axis is 0.68, rather than 0.0. This change makes bin edges less
likely to fall near fragment peak locations. The default bin width
has also changed from 1.001141 to 1.000508
-
The log file now includes information about the date and time that the
command was issued, the name of the computer on which the command was
run, and the elapsed wall clock time at the end of the run.
-
The command line option
--version T
has been replaced
with a command crux version
that prints the version
number to standard output and then exits.
-
The header for the feature file produced optionally by
crux percolator
and crux q-ranker
now includes names
for the first two columns, scan number and label (i.e. target or decoy peptide).
Version 1.30
May 5, 2010
Major enhancements
-
A new command,
xlink-search
, has been added. This command
searches a collection of spectra against a sequence database, finding
cross-linked peptide matches. The algorithm was described in the
following article:
Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and
William Stafford
Noble. "Detecting
cross-linked peptides by searching against a database of cross-linked
peptide pairs." Journal of Proteome Research. 2010.
-
A new search command,
sequest-search
, was added. The
original command, search-for-matches
, behaves as before
except that no .sqt files are printed and no Sp scoring is performed.
The new sequest-search
emulates SEQUEST®
searching. It first scores all candidate peptides with the Sp score,
then ranks and filters the results by that score, scoring the
remaining candidates with xcorr. Results are printed to .txt and .sqt
files.
-
The .mzXML file format is now supported for crux search-for-matches
and crux sequest-search when the
--use-mstoolkit
option
is set to TRUE.
-
The .csm output files from
search-for-matches
are no
longer produced and post-search operations take .txt files as input.
Minor changes
-
Replaced
mass-window
parameter with
precursor-window
and added precursor-window-type
for selecting windows of type mass, m/z, or ppm.
-
The
feature-file
option is now true/false instead of
taking a file name. The file is named '<fileroot>.<qranker|
percolator>.features.txt'. A header with the column names was
added to the file.
-
The new option,
--scan-number
, performs a search on a
specified subset of the spectra in the given file.
-
When only one decoy file is produced, the name is now 'decoy.txt'
instead of 'decoy-1.txt'
-
In the .txt files, protein names are now followed by the start index
of the peptide.
-
Modified sequences are reported differently in the .txt files.
Instead of modifications being represented by symbols (*,@,#, etc.)
they are indicated with the mass shift of the modification within
square brackets. As before, the modification information follows the
residue that is modified. If multiple modifications appear on one
residue, the masses may either be summed together or printed
separately in a comma separated list. This behavior is controlled by
the
--display-summed-mod-masses
option.
-
The modified decoy sequences are generated differently. Before, all
modified peptides were generated and each one was shuffled to create a
decoy peptide. Now a peptide is shuffled once for each peptide_mod
and all modifications are applied to that same shuffled peptide.
-
The 'percolator rank' column is now based on percolator scores instead
of percolator q-values. For cases where two PSMs have different
percolator scores but the same q-value, the ranks will reflect the
score differences.
-
The Weibull parameters used for computing p-values are now printed to
the .txt files.
-
The reporting of DeltaCn has changed. For PSMs of rank i, deltaCn
used to computed be as deltaCn_i = (xcorr_0 - xcorr_i) / xcorr_0.
Thus, deltaCn for the top-ranked PSM was always 0. Now deltaCn_i =
(xcorr_0 - xcorr_i+1) / xcorr_0. This change only
affects
search-for-matches
,
not sequest-search
. It also means that
q-ranker
and percolator
use the correct
DeltaCn values.
-
A new command,
print-processed-spectra
, performs
XCorr-style pre-processing on all spectra in a given file.
-
A small bug was fixed, in which even if the user requested average
mass, the search programs still used monoisotopic mass in the
calculation of XCorr and Sp.
-
Protein fasta files are now parsed protein-by-protein so that parsing
large files does not use excessive amounts of memory.
-
A limit was removed on how many peptides a protein can produce.
-
Crux is now built with g++ instead of gcc.
Version 1.22
September 16, 2009
Major enhancements
-
Crux is now distributed in two versions, a full version that is
covered by the same type of license as before (free to non-profit
users, and via a licensing fee to commercial users), as well as a
stripped-down version that is released under an open source license.
The stripped-down version does not include the database search
functionality but does include all of the post-processing tools. We
are unable to release the entire Crux package under an open source
license due to intellectual property issues. Both versions of Crux
are available via the Crux web
page: http://noble.gs.washington.edu/proj/crux/.
-
A new tool, q-ranker, is available for estimating peptide-spectrum
match q-values. This tool was described in the following article:
Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William
Stafford Noble. "Improvements to the Percolator algorithm for peptide
identification from shotgun proteomics data sets." Journal of
Proteome Research.
-
Version 1.05 of
percolator
has now been integrated into
the Crux source tree. A separate installation
of percolator
is no longer needed for basic
percolator
functionality. Note, however,
that percolator
remains under active development. You
may therefore wish to install the current, stand-alone version
of percolator
and run it separately to take advantage of
new features.
Minor changes
-
The internal normalization of the observed spectra has been modifed to
drop those peaks whose intensity is less than 1/20 of the maximum
intensity in the spectrum. This brings the xcorr score
for
crux
into closer agreement with the xcorr score
for SEQUEST®.
-
Compute-q-values now generates three different q-values (1) from
p-values using an analytical null model, (2) from decoys and xcorr
using an empirical null model, or (3) from decoys and p-values using
an empirical null model. All three types of q-values are computed
when p-values and decoys are present in the search results.
-
A parameter file is now automatically written to the output
directory.
-
A log file recording messages sent to stderr has been added for
search-for-matches
, compute-q-values
,
and percolator
.
-
The
--use-mz-window
parameter is now available for
search-for-matches
. When enabled, peptides must be
within +/- 'm/z-window' of the spectrum m/z. The m/z-window value is
taken from mass-window
.
-
A numerical bug in the Weibull p-value calculation was fixed, which
had previously caused occasional erroneous NaNs to be output.
-
The Weibull estimated p-values generated
by
search-for-matches
are now returned as p-values
instead of as -log(p-value). The corresponding q-values returned from
compute-q-values
are also now returned without the -log
transform.
-
The
--precision
option has been changed to control the
total number of significant digits printed instead of the number of
digits after the decimal point. The default precision has changed
from 6 to 8.
-
The parameters estimated for the Weibull distribution (used for
computing p-values) now use the xcorrs from all PSMs for a spectrum
instead of a random selection of 500.
-
The estimation of Weibull distribution parameters requires a minimum
number of scored PSMs. In the previous version, spectra with fewer
PSMs than the minimum were not given a p-value. Crux will now
generate extra decoys until there are enough scores.
-
The p-values for decoy PSMs are now generated from the same Weibull
distribution parameters as are used for the targets of the same
spectrum.
Version 1.21
May 14, 2009
-
The output for
search-for-matches
,
compute-q-values
, and percolator
has been revised extensively.
crux
will now create a directory, and all output files
will be created in that directory.
By default the directory will be named crux-output
,
but this can be changed using the new output-dir
option.
The output files for search-for-matches
will be:
search.target.csm
search.decoy-?.csm
search.target.sqt
search.target.txt
The output files for compute-q-values
will be:
qvalues.target.sqt
qvalues.target.txt
The output files for percolator
will be:
percolator.target.sqt
percolator.target.txt
-
The
fileroot
option has been added.
This option is used to specify a string which will be added as a prefix
to all output files.
-
The option
cleavages
was replaced with two
options, enzyme
which specifies the name of an enzyme
(e.g.trypsin) and digestion
which indicates
the degree of specificity, partial or full digest. The full list of
available enzymes is in the html docs and in the usage statement.
See also custom-enzyme
below.
-
The option
custom-enzyme
allows users to define arbitrary
digestion rules. This overrides the enzyme
option.
Syntax for the custom digestion rule is the same the syntax used by
X!Tandem and is described in the html docs.
-
The number of PSMs per spectrum printed to the output files is now
controlled by one option,
top-match
. This
makes max-sqt-result
obsolete.
-
It is now possible to control how many decoy sequences are generated
and in which file(s) they are returned. There is a new
option,
num-decoys-per-target
, which can be used to
generate more than one shuffled peptide per spectrum. This
replaces number-decoy-set
.
-
A new option,
decoy-location
has been introduced. The
three possible values are 'target-file' where all PSMs (target and
decoys) are sorted together for each spectrum and returned in one
file, 'one-decoy-file' where target PSMs are printed to one file and
all decoys are printed to another, and 'separate-decoy-files' where
there are as many decoy files as there are decoys per target.
-
Protein names for decoy matches are now prepended with 'rand_' in the
SQT files as in
'L rand_Y45678'.
-
The option
unique-peptides
only applies
to crux-generate-matches
. Each peptide is stored in the
index exactly once with references to all protein sources. Searches with
fasta files print each peptide only once.
-
The precision of the masses and scores printed to the sqt and text
files can now be specified by the user. The default precision changed
from 2 to 6.
-
Search progress is now reported by printing every 10th spectrum that is
searched. The verbosity can be adjusted with the parameter
print-search-progress
.
-
Decoy (shuffled) sequences now keep the first and last residue the
same as the target sequence that was shuffled to produce it. This is
a reversion to previous behavior.
-
It is now possible to skip the Sp score and score all PSMs with xcorr.
The default procedure is still to score all peptides for one spectrum
with Sp, rank by Sp, and eliminate all but the best-ranking PSMs (by
default, the top 500). The remaining PSMs are scored by xcorr,
re-ranked by xcorr and the top results returned. By setting
max-rank-preliminary=0, the Sp scoring is skipped and xcorr is
computed for all PSMs.
-
A new parameter
reverse-sequence
can be used to generate
decoy peptides by reversing them rather than shuffling. The first and
last residues are left unmoved. If the sequence is a palindrome ,
then a decoy will be generated by shuffling and a note to that effect
will be printed at the DETAILED INFO level of output (verbosity =
40).
-
P-values are now computed for decoy peptides.
-
The algorithm used to calculated the xcorr score has been modified so
that xcorr score will be in better agreement with scores generated by
SEQUEST®.
Version 1.20
January 6, 2009
-
Generating peptides and searching with up to eleven different dynamic
modifications is now possible. New options associated with this
feature are mod, cmod, nmod, max-mods, max-aas-modified.
-
The format of the .csm files has changed and files written by older
versions of crux are not readable with crux version 1.2.
-
When the option
cleavages
is set to all
,
peptide generation ignores all tryptic cleavage sites, effectively setting
the missed-cleavages
option to TRUE
regardless of user settings.
-
When one spectrum has identical xcorr scores for different sequences,
the rank of all those matches will be the same. Matches with the next
highest score will rank one below.
-
The options for setting the preliminary and primary score type have
been removed and are fixed as Sp and xcorr, respectively. A new
option,
compute-p-values=<T | F>
, was added to
control p-value computation.
-
The SQT file contains the spectrum calculated mass instead of observed
mass/charge on the S line.
-
There is now a test for confirming that the file downloaded from the
crux website was not corrupted. See installation instructions for
details.
-
Calculating a p-value requires a minimum of 40 matches. Spectra with
fewer than 40 matches will have p-value scores returned as NaN and a
warning will be printed at the DETAILED_INFO level (40) of verbosity.
-
Fixed error in generating neutral-loss peaks created as part of the
theoretical spectrum.
Version 1.02
December 1, 2008
-
Three programs,
crux-create-index
,
crux-search-for-matches
,
and crux-analyze-matches
, were merged into one program
named
crux
.
-
Percolator is now truly optional as all Crux programs will build
without it.
-
Fragment masses can now be calculated as average or mono-isotopic.
This is controlled by the
fragment-mass
option in the
parameter file.
-
The name of the score-type option that calculates p-values was changed
from xcorr-logp to xcorr-pvalue.
-
SQT files have two new lines in the header which describe the
arrangement of values in the results.
-
HTML documentation was updated to reflect the above changes.
Version 1.01
Hoopmann et al. Journal of Proteome Research, 2015.
assign-confidence
. More details are available in
"Progressive
calibration and averaging for tandem mass spectrometry statistical
confidence estimation: Why settle for a single decoy?".file-column
option added.feature-file-in
option to Percolator and
added top-match-in
, train-best-positive
and
spectral-counting-fdr
options.tide-index
command.tide-search
command now supports threading. See the
num-threads
parameter for details.pipeline
command to run a series of commands, and
the cascade-search
to run searches across a series of
databases.calibrate-scores
to assign-confidence
and completely revamped its
functionality.search-for-xlinks
command offers parameters to
control categories of
candidates: xlink-include-inter
, xlink-include-intra
,
and
xlink-include-inter-intra
.peptide-centric-search
option to tide-search.temp-dir
option
to tide-index
.create-docs
, subtract-index
,
and psm-convert
were added to Crux.generate-peptides
application has been revamped.barista
that occurred when the number of
peptides exceeded the number of PSMs.tide-search
when units
are m/z.hardklor
and bullseye
now use standard logging.percolator
, comet
, and boost
are shown
in the output of the version
command.feature-in-file
parameter added to percolator
.seed
parameter for percolator
has been renamed
to percolator-seed
.comet
exits with return code 1 on failure, rather than 0.use_sparse_matrix
changed to 1
.use-neutral-loss-peaks
changed to true
.xlink-score-method
parameter added to xlink-score-spectrum
.tide-search
tab-delimited output.PostProcessProtein.cpp
.Mix-max
procedure is updated to handle ties among target and decoy scores.use-neutral-loss-peaks
changed to true
Exact p-value
calculation takes into account the flanking and neutral loss peaks. output_percolatorfile
option is turned on. Previously, the file was named "comet.tsv"; now
it is "comet.target.pin."Assign-confidence
can take multiple input files.
comet
command can take multiple input files.
sidak
option has been added
to assign-confidence
to perform a Sidak adjustment.
peptide-level
option has been added
to assign-confidence
.
mz-bin-offset
has been changed from
0.68 to 0.40.percolator
command outputs the pout
XML format
again (controlled by the pout-output
parameter).percolator
command can output its native output by using the
original-output
parameter.tide-search
causing it to fail when
remove-precursor-peak
removed all peaks in a spectrum.max-precursor-charge
parameter
for tide-search
has been introduced.read-tide-index
command, which reads an index produced
by tide-index
and prints a list of peptides it contains.stop-after
option to print-processed-spectra, which
controls the point at which to stop preprocessing.tide-search
command now accepts multiple spectrum input files.
use-z-line
option to specify whether precursor
information is taken from the S or Z line when parsing MS2 files using
ProteoWizard.percolator
command.tide-search
command may now accept a FASTA database in
place of the index, in which case tide-index
will be run prior to
the search. The store-index
option allows the generated index
to be saved.assign-confidence
command will automatically detect
score type if the score
parameter is not specified, searching for
xcorr, e-value, or exact p-values.cascade-search
will report the source index database of the
peptide for all identified PSMs.top-match
parameter has been removed from
cascade-search
.Assign-confidence
has got new options: "combine-modified-peptide"
and "combine-charge-states".Assign-confidence
now supports top-match>1 in peptide-level filtering
mode.Assign-confidence
can use smoothed-p-value scores for PSM ranking.Assign-confidence
now does not carry out target-decoy competition in
peptide-level filtering mode.xlink-assign-ions
and xlink-score-spectrum
commands.assign-confidence
.estimation-method=peptide-level
case in assign-confidence
.search-for-xlinks
, xlink-assign-ions
and xlink-score-spectrum
parameters of the form
"use-a-ion" for a, b, c, x, y, and z-ions.allow-dups
option to tide-index.tide-search
command now supports calculation of exact
p-values via dynamic programming, as described
in this
article. The p-value calculation is controlled with
the exact-p-value
parameter.search-for-xlinks
now supports variable modifications and
larger protein databases. This new code is disabled by default, but
can be turned on by setting the
parameter use-old-xlink=F
.mz_bin_offset
has been changed to 0.40 from 0.68.centroided
parameter for the hardklor
command is
now implemented.spectrum-format
parameter for the bullseye
command
works properly.tide-search
command now uses information from the Z line rather
than the S line when reading spectrum files in the MS2 file format.tide-search
command now accepts the
spectrum-parser
parameter.protein-database
parameter
to spectral-counts
now only accepts fasta files. Parsing
of a protein index is no longer supported.spectral-counts
command that prevented
tide-search
output files from being parsed correctly.default-direction
parameter now takes a string value of the feature
name rather than an integer.
mz-bin-width
and mz-bin-offset
have been added
to tide-search
.clip-nterm-methionine
, keep-terminal-aminos
, and min-mods
have been added to tide-index
.
use-flanking-peaks
and use-neutral-loss-peaks
have been added to
tide-search
.tide-index
only generates peptides and sorts them,
leaving the generation of theoretical peaks to be done entirely on the
fly by tide-search
.tide-search
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 print-search-progress
parameter.calibrate-scores
command now outputs files with the stem
"calibrate-scores" rather than "qvalue."use-flanking-peaks
parameter now has a default value of
false.version
command now outputs the revision number.
make-pin
, is provided to create
input files for use by Percolator.spectrum-min-mass
and spectrum-max-mass
options have been renamed to spectrum-min-mz
and
spectrum-max-mz
, respectively.spectrum-parser
option was added to q-ranker
and
barista
.q-ranker
and barista
when
reading peptides with modifications.q-ranker
tab delimited output so that, for a
given peptide, flanking amino acids are reported for each protein that
contains that peptide, rather than only reporting one set of flanking
amino acids.percolator
, wherein the first and last
two characters were being truncated from peptide sequences when the
input was missing the flanking amino acids or when the charge state
was not indicated in the PSM IDs.calibrate-scores
no longer requires a protein input.calibrate-scores
now only takes the top match per
spectrum and charge.get-ms2-spectrum
now prints z-lines with Bullseye
files.The formula that is used to convert fragment m/z values from real
numbers into integers was modified. Previously, the conversion was
floor( (x / mz-bin-size) + 0.5 + mz-bin-offset )
The new conversion formula is
floor( (x / mz-bin-size) + 1.0 - mz-bin-offset )
The default values of the two parameters (mz-bin-size and mz-bin-offset) have not changed. The allowed range of the mz-bin-offset parameter was previously [-1,1], but has been changed to [0,1].
To understand the motivation for the changed formula, note that the mz-bin-offset parameter controls the location of bin edges, relative to integer masses on the mass scale. In general, mz-bin-offset should be chosen so that bin edges fall between the expected clusters of fragment masses. For fragments with 1+ charge, masses will cluster near integer values (after dividing by mz-bin-width), and the ideal value of mz-bin-offset would be 0.5. For mixtures of fragments with 1+ and 2+ charges, masses will cluster near integer and half-integer values, so mz-bin-offset near 0.25 or 0.75 would produce bin edges that best avoid the clusters of fragment masses. The old conversion formula did not correctly locate bin edges, given a chosen mz-bin-offset. The new conversion formula produces a proper translation of mz-bin-offset into bin edge locations.
seed
parameter is now available to control the
seeding of random number generator. The default value is 1.
seed
is available as a parameter from all applications.
It can be set as a command line option for
crux search-for-matches
and
crux percolator
.
decoys
parameter for crux
search-for-matches
was incorrectly documented. The default is
actually peptide-shuffle
, but the documentation said the
default was protein-shuffle
. The documentation has been
corrected.xcorr rank
in barista and
q-ranker feature files has been corrected to xcorr score
.
qranker_output.xml
has been renamed to
qranker.xml
.
deltaCni = (xcorr1 - xcorri+1) / xcorr1
it is now computed using
deltaCni = (xcorri - xcorri+1) / max(xcorri, 1.0)
--sqt-output <T|F>
(search-for-matches)--mzid-output <T|F>
(search-for-matches, percolator)--pinxml-output <T|F>
(search-for-matches)--pepxml-output <T|F>
(search-for-matches, q-ranker, barista, percolator)--txt-output <T|F>
(search-for-matches, q-ranker, barista, percolator)
txt-output
.
spectrum-parser=pwiz
to enable Proteowizard parsing.cmake
for the build process rather than
autoconf
/automake
.
crux
search-for-matches
.
crux create-index
on Windows and Cygin
that caused the program to fail with the message:
WARNING: Cannot rename directory FATAL: Failed to create index
protein database
is now an option rather than a required argument for crux spectral-counts
.
crux spectral-counts
.
crux spectral-counts
.
crux create-index
on Windows and Cygwin that caused it to fail on Windows and Cygin.
- Barista and Q-ranker accept search results in tab-delimited format, in addition to SQT format.
- Barista now reports posterior error probabilities, in addition to q-values, for PSMs, peptides and proteins.
- Barista's pep.xml output has been updated to be compatible with the TransProteomic Pipeline (TPP).
sequest-search
command has been removed. The
functionality of this command is still available using options for
the search-for-matches
command (see
the frequently asked questions list for
details).crux predict-peptide-ions
calculates the mass shift
resulting from the nh3 or h2o neutral loss correctly. Previously, a
neutral loss resulted in an addition of mass rather than subtraction.
crux predict-peptide-ions
reports ion-type as
'b','y','a', or 'p' rather than a number (i.e. 0, 1, 2, 3).crux predict-peptide-ions
now only allows one type of
neutral loss modification per ion. Previously, multiple different
types of neutral loss could be applied simultaneously to a single
ion.neutral-losses
option was removed from crux
predict-peptide-ions
, due to its redundancy with the supported
the --nh3
and --h2o
options.crux predict-peptide-ions
supports 'bya' in the
--primary-ions
parameter, which will generate
the a-ion series in addition to the 'b' and 'y' ions.crux spectral-counts
now has an option to compute the raw
spectral count.crux spectral-counts
now has an option to compute dNSAF
values.crux spectral-counts
was fixed so that it now
properly normalizes the NSAF value.crux
search-for-xlinks
using the missed-cleavages parameter.
Previously, this was unsupported.crux-predict-peptide-ions
and crux-generate-peptides
applications have been integrated
into the main crux
application.display-summed-masses
has been replaced by
mod-mass-format
. With this option, there is a new format
for reporting modificiations: the mass in the square braces is that of the
preceeding amino acid plus the modification mass. This format is compliant
with TPP pep.xml output.crux compute-q-values
now reports posterior
error probabilities in addition to q-values. Consequently, the
command was renamed crux calibrate-scores
.q-ranker
pep.xml files.crux barista
, a tool for inferring protein
identifications.crux q-ranker
with new outputs and
command-line syntax.crux create-index
now generates and store decoy
peptides in the index. Decoys can still be generated on-the-fly when
searching .fasta files.cterm-fixed
and nterm-fixed
, allow fixed terminal peptide
modifications, i.e., a mass shift applied to every peptide on either or
both termini.--mz-bin-width
and
--mz-offset parameters so that --xcorr-var-bin
is no longer needed.tide-results
utility, including
- Text format with user-specifiable fields.
- SQT format.
- PepXML format.
- Choose whether to display all proteins in which each peptide occurs or just one representative.
tide-index
. Index files created by previous versions
of Tide should not be used with the new version.missed-cleavages
option to allow specifying
the maximum number of missed cleavages in a peptide rather than
specifying none/any.crux
spectral-counts
when the input PSM file does not contain the
required q-values.use-flanking-peaks
, allows these to be
either on or off. Flanking peaks are by default in
crux sequest-search
but are not used by default
in crux search-for-matches
.crux spectral-counts
command for estimating
protein quantification.crux search-for-matches
and crux
sequest-search
can now take advantage of accurate precursor
masses in MS2 files generated by Bullseye (Hsieh et al. J. Proteome
Res. 9(2):1138-43, 2010).pep.xml
file header produced by Crux compatible
with the Transproteomic Pipeline.nterm
option to the link argument of crux
search-for-xlinks
.--peptide-list
has been added to crux
create-index
. When set to T, this option causes an ASCII
file of peptides to be included in the output directory. Each line
of the file lists the peptide sequence and its neutral mass.--compute-sp
has been added to crux
search-for-matches
. When set to true, all candidate peptides
will be scored by Sp in addition to xcorr. This option is recommended
for generating input to percolator
or q-ranker
.max-ion-charge
parameter to designate the maximum
charge for theoretical ions in crux search-for-xlinks
and
crux xlink-assign-ions
.
mass-precision
option which sets how many digits
are written for all mass and m/z values in .txt, .sqt, and .ms2 files.
crux
command being run and the settings so that unused
columns are not printed.
crux percolator
) based on fileroot. Now
files with different fileroots can be analyzed together.
compute-q-values
, percolator
and q-ranker
was modified to allow the programs to read
from and write to separate directories.--min-peaks
has been added to set a filter
for the minimum number of peaks a spectrum must have in order for it
to be searched. The default minimum is 20 peaks.--xcorr-var-bin
has been added to toggle the
new binning of the m/z axis. The default bin offset was returned back
to 0, but the default bin width is still 1.000508. (Note: this
erroneous change was subsequently reverted in version 1.34.)
--max-ion-charge
now places a limit on the
maximum charge state of the ions generated for the xcorr theoretical
spectra for crux search-for-xlinks
. This change is also
supported by xlink-assign-ions
.
--no-xval
was added to q-ranker, allowing
faster execution by skipping the internal cross-validation to select
hyperparameters.prevents cleavage
and
prevents cross-link
have been added to variable modifications
and support has been provided for the "prevents cleavage"
sub-option.search-for-matches
command, but Tide has been completely re-engineered to achieve a
thousandfold improvement in speed while exactly replicating Crux XCorr
scores. Currently, Tide is not fully integrated with Crux, and is
available only in binary executable format.crux search-for-matches
(--mz-bin-width
and --mz-bin-offset
) to
allow control of the binning of the m/z axis.ion-tolerance
option was removed from the search
tools.--version T
has been replaced
with a command crux version
that prints the version
number to standard output and then exits.crux percolator
and crux q-ranker
now includes names
for the first two columns, scan number and label (i.e. target or decoy peptide).
xlink-search
, has been added. This command
searches a collection of spectra against a sequence database, finding
cross-linked peptide matches. The algorithm was described in the
following article:Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and William Stafford Noble. "Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs." Journal of Proteome Research. 2010.
sequest-search
, was added. The
original command, search-for-matches
, behaves as before
except that no .sqt files are printed and no Sp scoring is performed.
The new sequest-search
emulates SEQUEST®
searching. It first scores all candidate peptides with the Sp score,
then ranks and filters the results by that score, scoring the
remaining candidates with xcorr. Results are printed to .txt and .sqt
files.--use-mstoolkit
option
is set to TRUE.search-for-matches
are no
longer produced and post-search operations take .txt files as input.
mass-window
parameter with
precursor-window
and added precursor-window-type
for selecting windows of type mass, m/z, or ppm.
feature-file
option is now true/false instead of
taking a file name. The file is named '<fileroot>.<qranker|
percolator>.features.txt'. A header with the column names was
added to the file.--scan-number
, performs a search on a
specified subset of the spectra in the given file.--display-summed-mod-masses
option.search-for-matches
,
not sequest-search
. It also means that
q-ranker
and percolator
use the correct
DeltaCn values.
print-processed-spectra
, performs
XCorr-style pre-processing on all spectra in a given file.Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William Stafford Noble. "Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets." Journal of Proteome Research.
percolator
has now been integrated into
the Crux source tree. A separate installation
of percolator
is no longer needed for basic
percolator
functionality. Note, however,
that percolator
remains under active development. You
may therefore wish to install the current, stand-alone version
of percolator
and run it separately to take advantage of
new features.crux
into closer agreement with the xcorr score
for SEQUEST®.search-for-matches
, compute-q-values
,
and percolator
.--use-mz-window
parameter is now available for
search-for-matches
. When enabled, peptides must be
within +/- 'm/z-window' of the spectrum m/z. The m/z-window value is
taken from mass-window
.search-for-matches
are now returned as p-values
instead of as -log(p-value). The corresponding q-values returned from
compute-q-values
are also now returned without the -log
transform.--precision
option has been changed to control the
total number of significant digits printed instead of the number of
digits after the decimal point. The default precision has changed
from 6 to 8.search-for-matches
,
compute-q-values
, and percolator
has been revised extensively.
crux
will now create a directory, and all output files
will be created in that directory.
By default the directory will be named crux-output
,
but this can be changed using the new output-dir
option.
The output files for
search-for-matches
will be:
search.target.csm
search.decoy-?.csm
search.target.sqt
search.target.txt
compute-q-values
will be:
qvalues.target.sqt
qvalues.target.txt
percolator
will be:
percolator.target.sqt
percolator.target.txt
fileroot
option has been added.
This option is used to specify a string which will be added as a prefix
to all output files.
cleavages
was replaced with two
options, enzyme
which specifies the name of an enzyme
(e.g.trypsin) and digestion
which indicates
the degree of specificity, partial or full digest. The full list of
available enzymes is in the html docs and in the usage statement.
See also custom-enzyme
below.
custom-enzyme
allows users to define arbitrary
digestion rules. This overrides the enzyme
option.
Syntax for the custom digestion rule is the same the syntax used by
X!Tandem and is described in the html docs.
top-match
. This
makes max-sqt-result
obsolete.
num-decoys-per-target
, which can be used to
generate more than one shuffled peptide per spectrum. This
replaces number-decoy-set
.
decoy-location
has been introduced. The
three possible values are 'target-file' where all PSMs (target and
decoys) are sorted together for each spectrum and returned in one
file, 'one-decoy-file' where target PSMs are printed to one file and
all decoys are printed to another, and 'separate-decoy-files' where
there are as many decoy files as there are decoys per target.
unique-peptides
only applies
to crux-generate-matches
. Each peptide is stored in the
index exactly once with references to all protein sources. Searches with
fasta files print each peptide only once.
print-search-progress
.
reverse-sequence
can be used to generate
decoy peptides by reversing them rather than shuffling. The first and
last residues are left unmoved. If the sequence is a palindrome ,
then a decoy will be generated by shuffling and a note to that effect
will be printed at the DETAILED INFO level of output (verbosity =
40).cleavages
is set to all
,
peptide generation ignores all tryptic cleavage sites, effectively setting
the missed-cleavages
option to TRUE
regardless of user settings.
compute-p-values=<T | F>
, was added to
control p-value computation.
crux-create-index
,
crux-search-for-matches
,
and crux-analyze-matches
, were merged into one program
named
crux
.fragment-mass
option in the
parameter file.October 15, 2008
- A bug limiting the length of the name of an index file was fixed.
- Modifications were made so that Crux will build with version 1.05 of Percolator. This is the only supported version of Percolator.
-
Memory leaks in
crux-search-for-matches
were patched. -
The
--version
option was added.
Version 1.0
March 4, 2008
Initial release


Description: {{campaign.description}}
This map represents the feedback(s) received for this campaign in the last week per hour.


30-May-2017 | Milku
Hurrah! for Pets@Home.
I received my first letter through the post. It's probably a bit of an exaggeration to call it a letter, but Pets@Home addressed it to me and I'm thrilled.
It was an update from the Pets@Home VIP Club. Obviously, I'm a member because I am very important. And, although I mightn't like the term, I am a 'pet'. I actually think my humans signed me up because they like receiving money-off coupons rather than because they wanted me to network with other VIPs. But I'm not complaining because I received the mail and not them! I just hope they head off to the retail park and buy me something now.
Don't forget to prepare for the start of 30 Days Wild. My little humans aren't waiting for June. They're interacting with nature today. They're spending the day at a We Are Adventurers holiday club. I can't wait to hear all about it.


Location
Iceland is a remote island located in the North Atlantic Ocean on the Mid-Atlantic Ridge in Northern Europe. Check it out on the map below!
Iceland is a relatively large island in the Atlantic Ocean. The nearest neighbouring country is Greenland, just 286 km (180 miles) away, followed by the Faroe Islands 420 km (260 miles), Scotland 795 km (495 miles), and Norway 950 km (590 miles).
Iceland is the second largest island in Europe, following Great Britain, and the 18th largest island in the world. The island itself stretches across 103,000 km² (40,000 square miles), and is about the same size as Hungary and Portugal, or Kentucky and Virginia. At its widest, Iceland measures 500 km (305 miles) east to west and 300 km (185 miles) north to south. The coastline is 4,970 km.
Landscape
Source: VisitIceland.com
With almost 80% of the country uninhabited, much of Iceland's terrain consists of plateaux, mountain peaks, and fertile lowlands. There are many long, deep fjords and glaciers, including Europe's largest, Vatnajökull. The landscape is characterized by waterfalls, geysers, volcanoes, black sand beaches, and otherworldly steaming lava fields.
Iceland's highest peak is Hvannadalshnjúkur, standing 2,119 m (6,852 ft) above sea level. More than 11% of the country is covered by glaciers. Its landmass comprises glaciers (12,000 km²), lava (11,000 km²), sand (4,000 km²), water (3,000 km²), and pasture (1,000 km²).
Formed about 25 million years ago, Iceland is one of the youngest landmasses on the planet, and consequently home to some of the world's most active volcanoes. The island owes its existence to a volcanic hotspot created by a fissure in the Mid-Atlantic Ridge, where the Eurasian and American tectonic plates meet.
The landmass is still growing by about 5 cm per year, as it splits wider at the points where the two tectonic plates meet. The last volcanoes to erupt were Eyjafjallajökull in 2010 and Grímsvötn in 2011. Iceland even has the world's newest island, Surtsey, formed in a volcanic eruption in 1963.
Iceland Geography Images
Feel free to click on any image to view a larger version.


BankOfOlive
Staff Accounts
| Name | Type | Actions | |
|---|---|---|---|
| Amaka Emodi |<EMAIL_ADDRESS>| Admin |
|
| Chike Ibuzo |<EMAIL_ADDRESS>| Staff |
|
| John Doe |<EMAIL_ADDRESS>| Staff |
|
| David west |<EMAIL_ADDRESS>| Staff |
|
| Gordon brown |<EMAIL_ADDRESS>| Staff |
|
| Chulo Green |<EMAIL_ADDRESS>| Admin |
|
| Favour Tor |<EMAIL_ADDRESS>| Staff |
|


Resources
A resource can be viewed as a logical artifact accessible from a repository cache using group, name and version information. Resources are resolved to file paths using the following convention:
[cache]/[group]/[type]s/[name]-[version].[type]
Example resource descriptor:
<?xml version="1.0" encoding="ISO-8859-1"?> <index> <resource> <info> <group>log4j</group> <name>log4j</name> <version>1.2.8</version> <type>jar</type> </info> </resource> .... </index>


We’ve been spenting time together for the past 6 years, and we can’t be more grateful to be unite back when we are studying together in China.
But right now we just want to celebrate our journey to become husband and wives, as we’ve been through so much together, e wwanted to start a new journey to become more than just a couple, a family that wwill alwways stays together.
 He is commited to everything he loves, and i know in my gut that he will always be that someone that are trustworthy.
As for now i just wish He knew how amazing he is, no matter what the world tells him.
- Wanda write this
Wanda is everything great in my world, she is inspiring and always the most hard-working woman, I love her sso much to the point where i just want to spend the rest of my life with her.
For one wish for her is absolute happiness in her life, because she deserve everything for all the journey she walking through.
- Vicky write this
We’ve been spenting time together for the past 6 years, and we can’t be more grateful to be unite back when we are studying together in China.
But right now we just want to celebrate our journey to become husband and wives, as we’ve been through so much together, e wwanted to start a new journey to become more than just a couple, a family that wwill alwways stays together.
 He is commited to everything he loves, and i know in my gut that he will always be that someone that are trustworthy.
As for now i just wish He knew how amazing he is, no matter what the world tells him.
- Wanda write this
Wanda is everything great in my world, she is inspiring and always the most hard-working woman, I love her sso much to the point where i just want to spend the rest of my life with her.
For one wish for her is absolute happiness in her life, because she deserve everything for all the journey she walking through.
- Vicky write this
at Grand Mosque
Manohara Street, B - 2
Milan, Italy
at Hotel Mulia Bali
Seminyak, B - 2
Bali, Indonesia
Dresscode
Tropical Vibe Formal
Dress, Suit
1 NIGHT, 1 BREAKFAST TREAT
Hotel Mulia Bali is one of the famous hotel in Bali, Indonesia. We’re excited to show you our hospitality, so we provide you 1 suite bedroom that can fit for 2 people, and also equipped with a lot of facilities such as welcome drinks, hot water, a bottle of wine, and so on.
*Please mention vicky & wanda, when you reserve them
SEE LOCATION


Decrypt
They call her Encrypt's other half
Usage instructions
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If you're looking for text to use this on, try encrypting something here.
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Decryption key
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