Download StavroX

StavroX & MeroX 2.0

Tools for Identifying Cross-Linked Peptides with Mass Spectrometry

MeroX 2.0

Recent Version:MeroX 2.0
(StavroX included)

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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 & StavroX are now a single software tool


18.02.2020 - Update of MeroX (version 2.0)
Download NEW version here (.jar-version)

Recent changes include (Version

23.01.2020 - Update of MeroX
(Download previous Version:  MeroX2.0.1.3.exe or MeroX2.0.1.3.jar)

Recent changes include (Version

23.01.2020 - Update of MeroX
(Download previous Version:  MeroX2.0.1.2.exe or MeroX2.0.1.2.jar)

Recent changes include (Version

25.11.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.1.0.exe or MeroX2.0.1.0.jar)

Recent changes include (Version

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

08.08.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.0.7.exe or MeroX2.0.0.7.jar)

Recent changes include (Version

06.08.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.0.6.exe or MeroX2.0.0.6.jar)

Recent changes include (Version

25.05.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.0.5.exe or MeroX2.0.0.5.jar)

Recent changes include (Version

20.05.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.0.4.exe or MeroX2.0.0.4.jar)

Recent changes include (Version

Recent changes include (Version

15.05.2019 - Update of MeroX
(Download previous Version:  MeroX2.0.0.2.exe or MeroX2.0.0.2.jar)

Recent changes include (Version

08.05.2019 - NEW version of MeroX (StavroX included) (Version 2.0)

New functions in MeroX 2.0:

Optimized Scoring & FDR

New Functionalities:

Graphical User Interface



04.12.2017 - Bug-Fix of StavroX und MeroX! (Versions: StavroX and MeroX
(Download previous Versions StavroX 3.6.6 and MeroX 1.6.6 )
Recent changes include:

16.11.2017 - Bug-Fix of StavroX und MeroX! (Versions: StavroX and MeroX
Recent changes include:

05.11.2017 - Major Update of StavroX und MeroX!
(Download previous Versions StavroX 3.6.5 and MeroX 1.6.5 )
Recent changes include:

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 and MeroX )
Recent changes include:

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:

06.03.2015 - Update of StavroX und MeroX
(Download previous Versions StavroX 3.4.12 and MeroX 1.4.12 )
Recent changes include:

07.12.2014 - BUG-FIX in StavroX
(Download previous Versions StavroX 3.4.11 and MeroX 1.4.11 )

14.12.2014 - Update of StavroX and MeroX.

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:

11.06.2014 - Update of StavroX and MeroX.
Recent changes include:

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.