Download StavroX

StavroX & MeroX

Tools for Identifying Cross-Linked Peptides with Mass Spectrometry


Recent Version:
StavroX 3.6.0
MeroX 1.6.0


This is the official web site for the Cross Linking-Mass Spectrometry Analysis Tools StavroX (2) and MeroX (1). Both software solutions can be used to identify cross links of peptides in complex mixtures. StavroX identifies all kinds of cross linked peptides (with DSS, BSł, Disulfides, zero-length...), while MeroX identifies cross links of cleavable cross linkers (CID-cleavable). You can Download both programs from this site. If you have got questions concerning one of both programs please visit the help section.

MeroX - Analysis of MS/MS-cleavable cross-linkers

MeroX is very similar to StavroX in that it identifies cross linked peptides. But MeroX is specialized for MS/MS-cleavable cross linking reagents (1)(3). MeroX identifies the specific fragmentation products of the cleavable cross links. This improves the reliability and simplifies the analysis enormously.


02.04.2015 - Major Update of StavroX und MeroX!

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!
- 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
- added support for z' and z'' ions
- Quicker analysis of large datasets
- Bug-Fix in Spectrum View

07.12.2014 - BUG-FIX in StavroX
- 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. 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. New features have been included to both programs:
- 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
- Pre score 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:

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.

Main Analysis Window 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.