News
18.02.2020 - Update of MeroX (version 2.0)
Download NEW version here
(.jar-version)
Recent changes include (Version 2.0.1.4):
- Bug-Fix: Software property deletes files and shuts down in Batch mode
- Bug-Fix: minimum number of fragments per peptide now calculated during scoring, not prescoring.
- Bug-Fix: xiView-export issue with special characters in scan headers
- Deisotoping slightly optimized (isotopic signals must be >10% of previous isotopes intensity)
- Export-directory is stored
- In GUI, intraprotein cross-links and homeotypic cross-links are distinct
23.01.2020 - Update of MeroX
(Download previous Version:
MeroX2.0.1.3.exe or
MeroX2.0.1.3.jar)
Recent changes include (Version 2.0.1.3):
- Bug-Fix: RISEUP-mode crashing MeroX
23.01.2020 - Update of MeroX
(Download previous Version:
MeroX2.0.1.2.exe or
MeroX2.0.1.2.jar)
Recent changes include (Version 2.0.1.2):
- Bug-Fix: XiViewer export fixed
- Bug-Fix: correction of scan headers containing ','
- Molecule composition calculator added for peptide mass calculator tool
- Spectra with unannotated charge states accepted and screen for multiple charge states
- Standard settings updated and corrected
- Bug-Fix: MaxMissedCleavages Settings not stored upon saving settings
- Bug-Fix: XiViewer export fixed
- Toolsmenu updated to copy masses to clipboard
25.11.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.1.0.exe or
MeroX2.0.1.0.jar)
Recent changes include (Version 2.0.1.0):
- Bug-Fix: Low screen resolution fix (Settings window) - scrollbar added, window resizeable
- Bug-Fix: viewing of ions in deconvoluted spectrum
- Bug-Fix: Peptide score cut off in Quadratic mode introduced
- New Feature: Added XiView export function
- New Feature: Fasta sequences stored in result-file for export to XiViewer
- New Feature: Decoys can be saved to Result file (optional, see settings).
- New Feature: Copy to clipboard of calculated mass (Toolsmenu)
- New Feature: Random decoys are checked for randomness (Levenshtein distance of at least 4)
- New Feature: Global maximum missed cleavage settings added.
- Update: When adding Molecules by elemental composition (amino acids, modifications, cross-linkers) spaces are ignored.
- Update: DSSO standard settings updated to include water-loss of S-fragment (named T-fragment)
- Update: Only considering a1 to a4 ions
13.11.2019 - Added to the website: Frequently asked questions!
Over the years a number of question occurred quite often. We
collected a list of those together with some answers here
10.09.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.8.exe or
MeroX2.0.0.8.jar)
Recent changes include (Version 2.0.0.8):
- Bug-fix: Score represenation of Dead-end cross-links
- Bug-fix: PepScore corrected in RISEUP mode
- Bug-fix: loading detail window for dead-end cross-links
- Bug-fix: identification of last and first signal in spectrum
- Bug-fix: numbering for intrapeptidal cross-links corrected
in cross-link site table.
08.08.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.7.exe or
MeroX2.0.0.7.jar)
Recent changes include (Version 2.0.0.7):
- Bug-fix: score readout of older versions
- Command line option to export possible fragment ion masses
(-f)
06.08.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.6.exe or
MeroX2.0.0.6.jar)
Recent changes include (Version 2.0.0.6):
- Bug-fix: Different scores were shown in other views
(cross-link site combination panel and detail window)
- Bug-fix: Quadratic mode minimum peptide score fixed
- Bug-fix: Downwards compatibility to StavroX-files
25.05.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.5.exe or
MeroX2.0.0.5.jar)
Recent changes include (Version 2.0.0.5):
- New feature: All molecules can be entered by their mass, not
only by composition anymore
- Bug-fix: Quadratic mode fixed (specific minimum peptide
score is applied)
20.05.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.4.exe or
MeroX2.0.0.4.jar)
Recent changes include (Version 2.0.0.4):
- New feature: FDR curve displayed in Decoyframe
- Bug-fix: Double clicking on cross-link site combination
didn't change candidate table
- Update: Loading Decoy data in the background
- Update: Removed Option to exclude Mixed target-decoys
- Update: Removed Option to exclude decoy searches
Recent changes include (Version 2.0.0.3):
- Bug-fix: qValue calculation corrected
- Bug-fix: MS-settings window corrected
- Bug-fix: Low Resolution data can be searched
15.05.2019 - Update of MeroX
(Download previous Version:
MeroX2.0.0.2.exe or
MeroX2.0.0.2.jar)
Recent changes include (Version 2.0.0.2):
- Bug-fix: mzML-loading bug due to Base64-conversion (no
compatibility with openJRE at the moment)
- Bug-fix: protein-lengths loaded from zdb-analyzed files
- Bug-fix: default log-file set for batch mode
- Bug-fix: results filtered by Q-value upon loading the result
file
08.05.2019 - NEW version of MeroX (StavroX included)
(Version 2.0)
New functions in MeroX 2.0:
- Proteome-wide-mode for analysis of large datasets
- RISEUP-Mode, combining RISE and proteome-wide mode
Optimized Scoring & FDR
- Final Score extended by pepscores, prescore and delta-score
- Decoy sequences are now generated on peptide level
- FDR now calculated separately for intra-protein,
inter-protein, dead-end and intra-peptide cross-links
- FDR estimated with FDR = (TD-DD)/(TT)
- Score colored in Mainframe to indicate quality of the score
value
- Pepscore included as filter in quadratic mode
- Q-values listed in result table
- Pepscores and delta-score saved to result file.
- Prescore is calculated once per candidate (independently of
cross-link position)
- Final score and pepscores in graphical user interface
New Functionalities:
- StavroX functionalities completely included
- Precursor mass correction using MS1-data (for mzML and mzXML
data)
- Saving and loading pre-calculated peptide database (*.zdb)
from file
- Settings can also be loaded from previous result files
- Manual mass recalibration option for MS1 and MS2
- Cross-linker specific reporter ions included
- Result files can be combined via graphical user interface
- Minimum charge state of precursors can be selected (default:
2)
- Minimum number of fragments per peptide can be selected
(default: 4)
- Search can be reduced to unique peptides (I==L option for
unique peptide search)
- Unknown MS1 charge states can be handled by iterating
through different possible charge states
- Search for PTMs possible
- Compatibility to OpenJDK enhanced
Graphical User Interface
- Network Graph for analyses of multi protein assemblies or
proteome-wide analyses
- Protein sequence analysis tool included in Tool menu
(showing observable and cross-linkable peptides)
- Protein name display can be selected if Uniprot fasta files
are used (e.g. Uniprot-id, entry name, gene name)
- Added tabs to detail frame, so multiple spectra can be
opened in the same window
- Added 'Load default settings'-functionality
Improvements:
- Drastic reduction in memory usage (generation of temporary
files, if applicable)
- Parallelization of several functions to increase cpu-usage
efficiency
- Option to exclude internal cross-linker fragment ions with
mass modification of 0, -18 and -17
- Settings - Default minimum score set to 50, default mode set
to RISEUP mode
- only spectra with more than 25 signals are used for
searching.
- Intra/inter-protein highlighted in unique cross-link table
- ProteinNames are shown as Gene Names if possible (from fasta
Header in uniprot format)
- Prescore calculation optimized.
- included '-gui' option for cammand line use to supress
graphical error messages whenn running on clusters
- No. of spectra matching a unique site are listed
- Consecutive Sequences excluded also for isoforms!!
Bug-fixes:
- fixed major bug in xVis export
- fixed minor bug in deisotoping
- fixed minor bug with PDB-files not specifying chain number
- fixed minor bug with multiply occuring cross-links
- fixed minor bug when loading dead-end/intrapeptide
cross-links
- fixed minor bug with non-available parent directory in
command line version
- fixed minor problems with memory release
04.12.2017 - Bug-Fix of StavroX und MeroX! (Versions:
StavroX 3.6.6.6 and MeroX 1.6.6.6)
(Download previous
Versions StavroX
3.6.6 and MeroX
1.6.6 )
Recent changes include:
- Bug-fix: NullPointerException and AccesViolation at the end
of Analysis
- Bug-fix: ConcurrentModificationException at the end of
Analysis
- Bug-fix: Wrong fragment for DSSO in Cross-link wizard
- Bug-fix: Non-encoded peptides (decoy sequences) were
reported for heavy/light cross-linker combinations
- Bug-fix: Missing isobaric candidates
- Added Error Message when Entering wrong Protease Site
- Added SDA as standard cross-linker (MeroX Wizard)
- Support for Bruker ProteinScape 4.0 MGF-Files implemented
- Default folder is location of executable
16.11.2017 - Bug-Fix of StavroX und MeroX! (Versions:
StavroX 3.6.6.5 and MeroX 1.6.6.5)
Recent changes include:
- Bug-fix: ConcurrentModificationException at the end
of Analysis
- Bug-fix: NullPointerException and IllegalArgumentException
at the end of Analysis
- Bug-fix: StavroX only - Non-encoded peptides (decoy
sequences) were reported for heavy/light cross-linker combinations
- Bug-fix: Wrong fragment for DSSO
in Cross-link wizard
- Added Error Message when Entering wrong Protease Site
- Added SDA as standard cross-linker (MeroX)
05.11.2017 - Major Update of StavroX und MeroX!
(Download previous Versions StavroX
3.6.5 and MeroX
1.6.5 )
Recent changes include:
- FDR-calculation adjusted to mixed decoys.
- Minor bug-fix to non-RISE-mode search algorithm
- Minor bug-fix to batch-mode
- Minor Changes to scoring algorithm
- Added option to add 2 other iontypes
- Added option to exclude consecutive Peptides (option not
considered in RISE-Mode)
- Included deviation into scoring
- Show only best scoring match in candidate Table! option to
show all remains
- Show Table of unique cross-linking sites
- Calculate distance of cross-links from PDB-Files and set
maximum bridged distance of cross-linker
- Improved cross-link-site determination
- Minor Bug-Fix in Detail window when selecting ions from the
table to be highlighted
- Several Dead-End Molecules can be defined (e.g H2O, NH3..)
- RISE mode optimization: RISE mode can now find incomplete
signal patterns
- Bug-fix in tables: changes are applied when clicking
somewhere in the GUI
- Bug-fix: Software does not close immediatly, if any result
file is still open
- Bug-fix: wrongly annotated Peptides in Detailsframe table
corrected
- Reporter Ions of known composition can be searched for
27.10.2017 - MeroX-Workshop at the 7th Symposium for
Structural Proteomics 2017 in Vienna (SSP 2017)
The new MeroX version was presented in the Cross-Linking-workshop
organized by the COST
action BM1403. The workshop material, including the presented beta
versions of StavroX and MeroX can be downloaded here.
The final release will be in November 2017 as the new functions still
need to be thoroughly tested.
02.04.2016 - Major Update of StavroX und MeroX!
(Download previous Versions StavroX
3.6.0.1 and MeroX
1.6.0.1 )
Recent changes include:
- Cross-linking data can be exported to xVis
- Calculation of probability of cross-linking sites in viewer
- Peptide backbone ions included in fragment view in StavroX
- Regular expressions can be used in filters (AND[..&...]
OR[..|..] NOT[!..])
- Zoom into spectra with mouse wheel
- Added save buttons to viewer
- Select-all checkbox in viewer
- Diagram for deviations of signals (can be hidden)
- Include semi-unspecific digest
- Negative ion mode supported
- Protease site can be blocked for cross-linking
- cRAP database included to probe for contaminants during
cross linking
- FDR cut off applicable
- Error files will not be overwritten if they're not empty
- Bug-fix: GUI (fragmentView stretched at higher charges)
- Bug-fix: Multiple cross-link candidates
- Bug-fix: Position of peptides
- Bug-fix: Scan number read from mzML files
MeroX-Presentation at HUPO 2015 - Poster Presentation of
StavroX and MeroX at the HUPO World Congress in Vancouver, Canada
September 27-30.
18.09.2015 - Major Update of StavroX und MeroX!
(Download previous Versions StavroX
3.5.1 and MeroX
1.5.1 )
Recent changes include:
- Search for intrapeptidal and dead-end cross link types
(types 0, 1) simplified
- Deisotoping algorithm implemented
- new identification algorithm: reporter ion scan event,
cross-linker reporter ions are identified first as prerequisite
- fragment view adjusted for intrapeptidal and dead-end cross
links
- Changes to scoring algorithm
- Tooltips and a Set-up Wizard help setting up the software
- Colors for ions can be customized
- Error information are redirected to external file Errors.txt
- Improved signal labeling for simpler manual inspection
06.03.2015 - Update of StavroX und MeroX
(Download previous Versions StavroX
3.4.12 and MeroX
1.4.12 )
Recent changes include:
- added support for z' and z'' ions
- Quicker analysis of large datasets
- Bug-Fix in Spectrum View
07.12.2014 - BUG-FIX in
StavroX
(Download previous Versions StavroX
3.4.11 and MeroX
1.4.11 )
- Decoy analysis and FDR calculation
might be corrupted in older versions! All analyses are correct. The
decoy analysis was not loaded completely for display. Therefore FDR
values might have been lower than actually determined! Already
analyzed datasets can be opened with this new version and decoy
analysis will be shown correctly!
- tab-delimited MGF files can be read
14.12.2014 - Update of StavroX and MeroX.
- Algorithm improvements
- Unspecific digest possible
- Analysis with light and heavy cross-linkers
- Minimum score threshold settable
08.08.2014 - Update of StavroX and MeroX.
(Download
previous Versions StavroX
3.4.5 and MeroX
1.4.5 )
New features have been included to both programs:
- new result file format applicable to large datasets (*.zhrs
and *.zhrm).
- *.hrs and *.hrm files are still supported! They will
be converted to the new format upon loading them
- Command line functionality added
- Spectra can be exported as EMF, EPS, JPG or PNG
- Merge-function for result files (only command line)
11.06.2014 - Update of StavroX and MeroX.
Recent
changes include:
- new result file format applicable to large datasets (*.hrs
and *.hrm).
- old result files cannot be loaded anymore. Either
perform the search again or use a previous version.
- Batch analysis possible in job queues
- Improved scoring algorithm
- Prescore option
- possibility to generate lists of calculated peptides, cross
links, inclusion list (Thermo Proteome Discoverer)...
- Small bugs fixed
01.04.2014 - Bug fix in MeroX! Issues with high precision
MS/MS-data and multiple neutral losses solved.
15.03.2014 - Bug fix in MeroX! Issue with detail window
solved.
03.03.2014 - Bug fix in MeroX! Issues with charge states of
cross linker fagment additions solved.
21.01.2014 - New Version of the cross linking software
packages StavroX (3.2.0) and MeroX (1.3.0) are available. The update
includes a faster identification of cross link candidates and faster
scoring. Scoring can be turned off or score quality can be increased.
StavroX obtained a new scoring algorithm.
18.11.2013 - MeroX 1.2.9 is now available! MeroX identifies
cross links specifically with MS-cleavable Cross linkers. New Version
of StavroX 3.1.19 adds *.mzML support.
06.11.2013 - New Version 3.1.18 - several features added:
- Mass search possible on all tables with Da, ppm or %
precision.
- compatibility to *.mzXML and *.pkl
file formats added.
- Better compatibility to MAC.
- Cancel button to abort calculation.
25.10.2013 - New Version 3.1.17 adds better perfomance to
zooming in spectra (rectangle drawn while dragging) and an automatic
and manual update check.
18.10.2013 - Bug fix of problem with Settings file
(duplication of lines), that was introduced with version 3.1.15. It
is now possible to run StavroX without calculating a score.
11.09.2013 - Minor changes to the score, the standard settings
file and the Settings window have been implemented in version 3.1.15.
The standard settings file that is created on the first start was
changed, as the EDC cross linker changes the mass by -H2O and not
zero.
30.08.2013 - StavroX 3 is published online. The new version
can be downloaded from the download page.
What is new in StavroX 3 ?
New Language: StavroX 3 was developed in Java from
scratch. It´s function is similar to that of previous versions (1).
Much faster: StavroX 3 runs more efficiently than
previous versions. It uses Multi-threading to split the time
consuming scoring of cross linking candidates to all availble
processors. StavroX 3 can handle more complex calculations than
before like more proteins or more complex modifications.
New Score: StavroX 3 uses a revised algorithm to
calculate the score of a cross linking candidate. The new algorith is
based on the probability of an ion to occure and the intensity of the
signal in the fragment spectrum.
New Fragmentation representation: On the right you
see the new fragmentation representation of a cross link. It shows
the identified fragment ions with their respective positions in the
peptide as well as the charge. The intensity of the identified ion is
color-coded. This makes it easy to identify ion series as well as the
identity of high intense signals.
New GUI: The Graphical User Interface (GUI) has
changed to present data in a more efficient way. For example: The
labeled spectrum is shown once a precursor is selected.
New Detail Window: In a detail window, all the
details of one specific cross link can be seen. This window also
contains the new fragmentation view of a cross link
More Settings: It is now possible to search for a,
b, c, x, y and z-ions. Neutral losses of fragment ions can be
specified.
Filter & Search: Handling of big datasets is
simplified by a number of filter and search options.
new File Formats Results of analyses are stored in a
more efficient way and take up less space on the hard drive.
