Hi William and Ye-Soon,
Firstly regarding the baseline correction. We have this working on a number of
PC's here and it works fine. The lowest spec machine is a Pentium Dual core 2.6
GHz with 4GB RAM
The developer who wrote this module is on holiday currently but I will ask when
he is back if he has any ideas why it fails. Please triple check you have the
startup batch file configured correctly. Also make sure you have installed the
R packages specified in your R system.
Here is my start-up batch file for comparison: (I use Win7 64bit). You will
have to put in your own paths to your R installation
=======================
@echo off
rem The HEAP_SIZE variable line defines the Java heap size in MB.
rem That is the total amount of memory available to MZmine 2.
rem Please adjust according to the amount of memory of your computer.
rem Maximum value on a 32-bit Windows system is about 1300.
set HEAP_SIZE=4096
rem The TMP_FILE_DIRECTORY parameter defines the location where temporary
rem files (parsed raw data) will be placed. Default is %TEMP%, which
rem represents the system temporary directory.
set TMP_FILE_DIRECTORY=%TEMP%
rem This is the home directory path for NIST MS Search. It should hold
rem nistms$.exe.
set NIST_MS_SEARCH_PATH=C:\NISTDEMO\MSSEARCH
rem Set R environment variables.
set R_HOME=C:\Program Files\R\R-2.11.1-x64
set R_SHARE_DIR=%R_HOME%\share
set R_INCLUDE_DIR=%R_HOME%\include
set R_DOC_DIR=%R_HOME%\doc
set R_LIBS_USER=%USERPROFILE%\My Documents\R\win64-library\2.11
rem Include R DLLs in PATH.
set PATH=%PATH%;%R_HOME%\bin
rem The directory holding the JRI JARs (JRI.jar, JRIEngine.jar REngine.jar).
set JRI_CLASS_PATH=%R_LIBS_USER%\rJava\jri
rem The directory holding the JRI shared library (libjri.so).
set JRI_LIB_PATH=%JRI_CLASS_PATH%
rem It is usually not necessary to modify the JAVA_COMMAND parameter, but
rem if you like to run a specific Java Virtual Machine, you may set the
rem path to the java command of that JVM
set JAVA_COMMAND=java
rem It is not necessary to modify the following section
set LOGGING_CONFIG_FILE=conf/logging.properties
set JAVA_PARAMETERS=-XX:+UseParallelGC -Djava.io.tmpdir=%TMP_FILE_DIRECTORY%
-Djava.util.logging.config.file=%LOGGING_CONFIG_FILE% -Xms%HEAP_SIZE%m
-Xmx%HEAP_SIZE%m -Dnist.ms.search.path="%NIST_MS_SEARCH_PATH%"
-Djava.library.path="%JRI_LIB_PATH%"
set
CLASS_PATH=MZmine2.jar;"%JRI_CLASS_PATH%\JRIEngine.jar";"%JRI_CLASS_PATH%\JRI.jar";"%JRI_CLASS_PATH%\REngine.jar"
set MAIN_CLASS=net.sf.mzmine.main.MZmineCore
rem Show java version, in case a problem occurs
%JAVA_COMMAND% -version
rem This command starts the Java Virtual Machine
%JAVA_COMMAND% %JAVA_PARAMETERS% -classpath %CLASS_PATH% %MAIN_CLASS%
rem If there was an error, give the user chance to see it
IF ERRORLEVEL 1 pause
==============================
Secondly many people ask in this forum how to get started with mzMine. I would
recommend the tutorial video it helped me a lot.
Just as a hint, below is a typical workflow I might use... We have Orbitrap
high resolution LC-MS. We also use mzMine for GCMS, the main difference being
the mz parameter is relaxed for GC to 0.5 Dalton. The best advice I can give is
to study the TIC plots closely to assess the noise level and minimum peak
heights before you start. You will also have to experiment with values to see
what works best with your own data. One of the new features we are adding is
the ability to save and load workflows from the Batch mode function as XML
files so this will make it easier to share workflows for particular instruments.
========================================
Typical workflow for UPLC-Accurate mass
========================================
Read in Thermo Raw Files
Mass detector
Wavelet transform
Noise level 1E4
Scale Level 10
ChromatogramBuilderModule
Mass listmasses
Min time span 0.01
Min height 100000.0
m/z tolerance 0.0050
DeconvolutionModule
Baseline cut-off
Min peak height">100000.0
Peak duration range <min>0.0 <max>1.0
Baseline level">10000.0
Then I will proceed to
Normalisation - RT normaliser
Join Aligner
Identification - Custom database search
Gap Fill
Then I will look for major unidentified peaks and maybe do individual
online database search
Finally save results Export - Export to CSV file
Best advice is to check results at each stage and make sure they are sensible
Good luck,
Mark
-- -----------------------------------------
Mark Earll
Research Leader - Metabolomics
Analytical Sciences
Syngenta
Jealott's Hill International Research Centre
Bracknell
Berkshire
RG42 6EY
United Kingdom
mark.ea...@syngenta.com
www.syngenta.com
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