Recent Version:MeroX 2.0
(StavroX included)
Question not in the list? Need help?If you need help setting up the analysis or are experiencing any bugs, please contact me via E-Mail to info(at)StavroX.com . If you need to send files (Fasta, MGF/mzML, Settings) please use TransferXL or Firefox send. |
There are several reasons, why MeroX could crash. If the next tip doesn't help, please send an email to info@stavrox.com.
One common reason can be memory restrictions. Try to start MeroX from the command line with more allocated memory. To do so, follow this quick guide:
- Download the newest MeroX verison as a jar file to your hard drive
(not onto a stick or a network folder)
- In the
same folder as the MeroX2.0.jar, create an empty text file
- In this file write the following line:
java
-Xmx8G -jar MeroX2.0.jar -l
- Save the file as
MeroX.bat (make sure it actually changed the file extension to
bat)
- double-click the MeroX.bat file. MeroX
should start as usual, but now with 8GB of RAM available to Java
(For editing text or bat files, I can recommend Notepad++)
MeroX can also be run on OpenJDK and has been tested with: AdoptOpenJDK 8
MeroX can be run from the command line of any operating system
with an installed java JRE. Details about how to run a single
analysis are in the help section (here).
If you want to run multiple searches with the same settings and
fasta file, but different mzML files, this can be automated with
short scripts (see link
here) These scripts have to be modified to suit the individual
need.
Try one of the following steps, to increase the speed of MeroX:
1. Copy MeroX and all required files (fasta, mzML,
properties.mxf) to a local hard drive and NOT on a usb stick or
server. File access times will limit the speed of MeroX
drastically otherwise.
2. Reduce the complexity of the
analysis:
- reduce the number of variable
modifications and miscleavages
- reduce the
number of proteins in the database (e.g. all proteins making up
80%-90% of all identified PSMs)
3. MeroX uses
multithreading, so running MeroX on a high performance computing
node (cluster) is feasible and also recommended
4. Run
one MS-file at a time. Even though multi-file processing is
possible, it is recommended to do the analysis separately and
merge the reults after completion.
This feature is only available from the graphical user interface. When selecting the MS-file for analysis, multi-file selection in the file dialog is enabled. When running from the command line, result files can be merged after analysis from the GUI.
MeroX will use all the resources that are allocated by the system. To reduce the load of MeroX on the system, so that it is possible to run longer MeroX analyses and still use the computer in parallel, the OS needs to specify the resources allocated to MeroX. In Windows the cores can be selected individually and are represented by a single hexadecimal value; the value 1F represents the first four cpus (for details see the links below.)
It can be done in windows by creating a shortcut (see a detailed
description here).
- Right click on the MeroX2.exe file and create a
shortcut.
- Right click the shortcut and go to
properties.
- edit the field 'Target:'
-
insert the following text before the target:
cmd.exe /c start /affinity 1F
- press ok.
To
set the same Icon as MeroX for this shortcut:
- Go
to properties again
- select 'Change icon' and
search for the MeroX executable file on your computer
-
Select the MeroX logo (should be the only one)
-
press ok.
It can also be done from the command line using the same affinity command in Windows and a similar command in Linux (see for Windows, for Linux).
LinuX:
taskset -c 0,1,2,3 java -jar
MeroX2.jar
Windows
start /affinity
1F java -jar MeroX2.jar
MeroX offers four different algorithms. The choice mainly depends on the cross-linker and the complexity of the sample.
Yes you can. You can download a zip-file containing high resolution images here. Please cite Götze et al. 2014.
StavroX is now part of the MeroX software. All functions of
StavroX have been included in the MeroX software. StavroX and
MeroX will therefore benefit from any advances that will be made
in the future. I made this choice with the new update of MeroX.
It makes sense to have a single tools for cross-linking/MS. From
a developers point of view, the two tools perform very similar
tasks and maintaining two tools in parallel isn't efficient.
Older versions of StavroX can still be downloaded from the News page.
In theory, MeroX can handle larger databases with non-cleavable linkers such as DSS/BS3 or BS2G. This is only possible, if a minimum peptide score is used as a prefiltering step. Set the minimum peptide score to values between 5 and 20 (e.g. 10) to test larger databases.
Adding custom modifications is possible in MeroX (See help for details). To define an unlisted modification, e.g oxidation of Tryptophane, follow this guide:
- Go to Settings/Amino acids (tab) You should see a table
of all presently listed amino acids
- Click Add
and enter the required information
- For name use
e.g. tryptophane oxidized
- For the code, select
a code from the dropdown box, e.g. 'y'. MeroX will differentiate
the case of the letter.
- The composition is the
elemental composition of the residue in a polypeptide chain (for
conventions see Composition)
- for
oxidized tryptophane enter C11H10N2O2
- press OK.
Now a new amino acid should be in the list.
- go
to the modification tab and below the variable modification
table, press the Add button
- Select From 'Y' and
to 'y' and max modification '1' and press OK.
Now MeroX
will search for tryptophane and oxidized tryptophanes
To add a new cross-linking reagent, go to Settings and then to
the Cross-Linker tab. Press the 'Add XL' button and enter all the
required information. MeroX allows you to enter the composition
of the linker after cross-linking. To retrieve this information I
can recommend to draw the chemical structure of the cross-linked
side chains before and after cross-linking and then compare the
composition. In the example below (EGS) the NHS esters react with
amine groups to form amide bonds. the composition of the two
amines before cross-linking is N2H4. after cross-linking the
composition is C10H14N2O6. The cross-linker will therefore add
C10H10O6.
Cross-links from NHS-esters occur between nucleophiles, most
notably lysines and N-termini but also hydroxy grous in serine,
threonine or tyrosine. As site specificity for both sites one can
enter 'K{' which represents lysine and the N-terminus or 'KSTY{'
which additionally represents the thre hydroxy-containing amino
acids.
For reactive amino acids such as photo-methionine, a new
amino acid residue should be added in the amino acids tab. For
photo-methionine, the composition of the residue would be
C6H9N3O. As single letter code one can pick any letter that is
unused (e.g. 'x'). Cross-links can occur from 'x' to any residue
('ABCDEFGHIKLMmNPQRSTVWY') via a carbene intermediate or to
acidic residues ('DE') via an intermediate diazo-compound to form
an ester. The resulting compositional difference is -N2 as
elemental nitrogen is leaving the reaction.
Yes, the settings that were used to generate a result file are saved within the result file. You can load the result just as any .mxf file from the Settings window. Alternatively you can open the result file with a zip-file manager (such as 7-zip) and extract the properties.mxf file manually.
Some options are only available under defined conditions. The RISE-mode for example is only available, if a cleavable cross-linker is selected that gives rise to at least one cross-linker fragment per peptide (make sure to check the essential check box for expected/required cross-linker fragments).
MeroX is only designed to detect cross-links of two peptides.
MeroX is only designed to detect cross-links of two peptides with a single cross-linker. One could add a dead-end cross-link as a modification of lysine residues into MeroX.
MeroX can handle the analysis of isotope labelled proteins (e.g. 15N isotopic labelling). To do so, it is necessary to set up light and heavy amino acids as upper case and lower case respectively in the settings and have the protein in the fasta file as upper and lower case. Then it is just important to also add protease sites and cross-linking sites to the heavy and light version. If you do the analysis, you can search for cross-links of L-L, L-H and H-H cross-links. See this link for an example settings and fasta file.
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