Dear Yee-soon,
I have recently had the task of installing a number of copies of mzMine 2.6 and
have a few modifications to the official setup instructions. It may be worth me
reproducing them here to make sure you have not missed anything.
It's also worth noting that you need a good deal of memory for baseline
correction. I have an 8GB machine and I set up at least 4GB for mzmine (HEAP
SIZE = 4096)
Also I tend to use 1 dalton bin width which works fine even with accurate mass.
Going below 0.5 width causes very large increase in processing time.
As Tomas has already mentioned you need to have set up R and downloaded the
additional packages [ install.packages(c("rJava", "ptw", "gplots")) ]
===================================
1.2. Installation and starting
===================================
Prerequisites
1. Install Java SE runtime (JRE) version 1.6 or later (available from
http://java.oracle.com)
2. (Optional) Install Java3D (available from http://java3d.java.net).
Java3D is required for the 3D visualizer module. On Mac OS X, Java3D is
pre-installed by default.
3. You then have the JRE installed and Java3D installed but the final
piece of the puzzle is to make sure that the JRE knows about Java3D by
installing Java3D as a Java extension. Determine where the JRE is installed,
e.g. C:\Program Files\Java\jre6 - let's call this JRE_HOME, and then copy the
JAR files from \Java\java3D\1.5.2\lib\ext to JRE_HOME\lib\ext and the DLL files
from \Java\java3D\1.5.2\bin (?) to JRE_HOME\bin. So, the directory structure
and files in \Java\java3D\1.5.2 should be replicated under JRE_HOME, e.g.
JRE_HOME\lib\ext\j3dcore.jar
JRE_HOME\lib\ext\j3dutils.jar
JRE_HOME\lib\ext\vecmath.jar
JRE_HOME\bin\j3dcore-ogl.dll
4. (Optional) Install R (http://www.r-project.org). R is required for
certain modules such as baseline correction or heat maps. The following
packages must be installed in your R distribution: rJava, ptw and gplots. To
install them, run the following command in R: install.packages(c("rJava",
"ptw", "gplots"))
5. (Optional) Install the MSFileReader library for reading Thermo RAW
files directly (see the section RAW file import). NB. I have found
msfilereader_ver-13_04-14-2009 works fine with mzmine but a later version data
12/12/2011 does not work with mzmine
MZmine 2 installation
1. Download the MZmine distribution and unpack it to a folder of your
choice.
2. A startup script is provided for MS Windows (startMZmine_Windows.bat),
Mac OS X (startMZmine_MacOSX.command) and Linux (startMZmine_Linux.sh)
environments.
3. Edit the startup script in a text editor and adjust the various
parameters, particularly HEAP_SIZE (amount of memory allocated for the Java
Virtual Machine), R_HOME (the path to R installation, if installed) and
JAVA_COMMAND (path to Java runtime start command).
============================================================================================
Mark
-- -----------------------------------------
Mark Earll
Research Leader - Metabolomics
Analytical Sciences (Office 102/65)
Jealott's Hill International Research Centre
Bracknell
Berkshire
RG42 6EY
United Kingdom
Direct +44 1344 414316
mark.ea...@syngenta.com
www.syngenta.com
-----Original Message-----
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Sent: 18 April 2012 05:33
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Subject: Mzmine-devel Digest, Vol 47, Issue 14
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Today's Topics:
1. Re: targeted peak detection (gegoe)
2. Re: (no subject) (YS LING)
----------------------------------------------------------------------
Message: 1
Date: Tue, 17 Apr 2012 03:17:08 -0700 (PDT)
From: gegoe <ge...@psb.vib-ugent.be>
Subject: Re: [Mzmine-devel] targeted peak detection
To: mzmine-devel@lists.sourceforge.net
Message-ID: <1334657828470-3916824.p...@n3.nabble.com>
Content-Type: text/plain; charset=us-ascii
Yeah, this looks great now :)!!
IS this new paramater in the latest version of mzmine 2.7.2?
And about my second question, did you get any information on that?
Cheers,
Geert.
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------------------------------
Message: 2
Date: Wed, 18 Apr 2012 12:33:11 +0800
From: YS LING <ling8...@gmail.com>
Subject: Re: [Mzmine-devel] (no subject)
To: Developer discussion <mzmine-devel@lists.sourceforge.net>
Message-ID:
<CAKSxhzNS1ETDv3XQfp9gbSP=No6uJFM3Y_2=nx-0rdqdaua...@mail.gmail.com>
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Hi Tomas,
Me again. Well I had tried a lot of things, including using different
computer to run the Baseline Correction but it doesn't seems to work at
all. I also don't know whats wrong with it.
Anyway i also encounter another problem regarding the Peak lists. Since i
collect these data from the Thermo instrument i wonder MZmine 2 cope with
Thermo data?
Following is my steps by steps.
1. I input my RAW data.
2. Then these data underwent scan by scan filtering - Resampling filter
(set the m/z bin at 0.5). This will generate a new raw data file named *.RAW
filtered*
3. Newly generated* .RAW filtered *file was selected for Peak Detection -
where Centroid with 5.0E3 noise level. From here Peak list *.RAW filtered
chromatograms* will be generated.
However, i double clicked this file and surprisingly found that there were
nothing on the list. (the attached pic).
I wonder is it related to my computer problem or the incompatibility of
MZmine with Thermo RAW files.
Thank you very much and sorry for keep bothering you.
[image: ???? 1]
YS LING <ling8...@gmail.com> ? 2012?4?17???12:24 ???
> Hi Tomas,
> I had cross checked the JRI_LIB_PATH variable. The problem is not solved.
>
> Tomas Pluskal <plus...@oist.jp> ? 2012?4?17???11:08 ???
>
> I mean this:
>> Open the startMZmine.bat script in a text editor (e.g. Notepad).
>> Find the JRI_LIB_PATH variable and check if it points to the correct path
>> where R is installed.
>>
>> Tomas
>>
>> On Apr 17, 2012, at 11:50 AM, YS LING wrote:
>>
>> I'm not quite sure what u mean by JRI_LIB_PATH variable in the script is
>> set correctly. Yes i had installed the R 2.15.0. But the problem still
>> remain.
>>
>> Tomas Pluskal <plus...@oist.jp> ? 2012?4?17???10:04 ???
>>
>>> Hmm, that is a bit strange.
>>>
>>> Do you have R installed?
>>>
>>> Please edit the startMZmine.bat script and check if the JRI_LIB_PATH
>>> variable in the script is set correctly.
>>>
>>> Tomas
>>>
>>>
>>> On Apr 17, 2012, at 10:38 AM, YS LING wrote:
>>>
>>> > Hi Tomas,
>>> >
>>> > After i imported the RAW data, I underwent Filtering > Baseline
>>> correction. I set the m/z bandwidth (eventhough if you don't change any
>>> parameter within) then i click OK, the MZmine program just shut down.
>>> >
>>> >
>>> >
>>> > Tomas Pluskal <plus...@oist.jp> ? 2012?4?17???8:57 ???
>>> > Hi Yee-Soon,
>>> >
>>> > Sorry I do not understand what do you mean by "automatic shutting
>>> down". Please describe the exact steps you have taken.
>>> >
>>> > Cheers,
>>> >
>>> > Tomas
>>> >
>>> >
>>> >
>>> > On Apr 17, 2012, at 9:53 AM, YS LING wrote:
>>> >
>>> >> Hi Tomas,
>>> >> I wonder if you have encounter the problem of automatic shutting
>>> down? When i tried to adjust the bin width (Raw Data Method > Data set
>>> filtering> Baseline correction > m/z band width = 0.03) and i just shut
>>> down and showed as following
>>> >> <image.png>
>>> >>
>>> >> Is there any thing wrong? Please do assist me. Thanks a lot.
>>> >>
>>> >
>>> > ===============================================
>>> > Tomas Pluskal
>>> > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>>> University
>>> > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>>> > TEL: +81-98-966-8684
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > Yee-Soon LING
>>> >
>>> ------------------------------------------------------------------------------
>>> > Better than sec? Nothing is better than sec when it comes to
>>> > monitoring Big Data applications. Try Boundary one-second
>>> > resolution app monitoring today. Free.
>>> >
>>> http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________
>>> > Mzmine-devel mailing list
>>> > Mzmine-devel@lists.sourceforge.net
>>> > https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>>
>>> ===============================================
>>> Tomas Pluskal
>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>>> University
>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>>> TEL: +81-98-966-8684
>>>
>>>
>>
>>
>> --
>> Yee-Soon LING
>>
>> ------------------------------------------------------------------------------
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
>>
>> http://p.sf.net/sfu/Boundary-dev2dev_______________________________________________
>> Mzmine-devel mailing list
>> Mzmine-devel@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel
>>
>>
>> ===============================================
>> Tomas Pluskal
>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
>> University
>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>> TEL: +81-98-966-8684
>>
>>
>
>
> --
> Yee-Soon LING
>
--
Yee-Soon LING
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