Re: [Mzmine-devel] Question concerning MZmine

[Ana Luísa/Guilherme]

Hi Tomas,

I still can not use MZmine for two reasons:

- The data that I have are in a csv file where the lines are scans and the columns are m/z. You have entered a software converter MassHunter .d to mzXLM, but my GC-MS data are not compatible in MassHunter. Do you know if there is another solution to solve this problem?
- I still can not put more than 900 MB of RAM in JAVA. My computer has 5GB of memory and when I open the MZmine I close all unnecessary software. What can I do to have more than 1 GB in JAVA?

ThanK you for your attention,

Ana Luísa

---

Em 18/07/2011 00:06, Tomas Pluskal < plus...@oist.jp > escreveu:
Hi Ana, 

Try using msconvert: http://proteowizard.sourceforge.net/tools/msconvert.html

Tomas

On Jul 18, 2011, at 9:05 AM, Ana Luísa/Guilherme wrote:

Hi Tomas,

I use a GC-MS Agilent. I exported my 3D data in csv format and converted to XML. The matrix rows correspond to the number of scan and the columns correspond to the masses of the ions.
How should the organization of the array of data to be read by MZmine?

I am willing to manually change my data arrays.

I read that it is necessary that the data is in format mzXML, netcdf, mzDATA or mzML. How is the format mzXML?

I have not tried to import my data because there is les s than 1 GB of RAM to run the calculations. I think tomorrow I solve this problem.

Thank you,

 

Ana Luísa

---

Em 16/07/2011 22:53, Tomas Pluskal < plus...@oist.jp > escreveu:
Hi Ana,

When you downloaded MZmine, you downloaded a ZIP file.

Did you extract the whole contents of the ZIP file to some folder?

Can you see MZmine2.jar file in that folder?

Tomas

On Jul 17, 2011, at 4:51 AM, Ana Luísa/Guilherme wrote:

MZmine developers,

 

I would like to use MZmine 2 to align and normalize data surfaces m / z X retention time.
I use Windows OS XP and when I click on the file startMZmine_Windows.bat the following dialog appears:

 

“java version "1.6.0_26"

Java(TM) SE Runtime Environment (build 1.6.0_26-b03)

Java HotSpot(TM) Client VM (build 20.1-b02, mixed mode, sharing)

Exception in thread "main" java.lang.NoClassDefFoundError: net/sf/mzmine/main/mz

mineclient/MZmineClient

Caused by: java.lang.ClassNotFoundException: net.sf.mzmine.main.mzmineclient.MZm

ineClient

        at java.net.URLClassLoader$1.run(Unknown Source)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(Unknown Source)

        at java.lang.ClassLoader.loadClass(Unknown Source)

        at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)

        at java.lang.ClassLoader.loadClass(Unknown Source)

Could not find the main class: net.sf.mzmine.main.mzmineclient.MZmineClient.  Pr

ogram will exit.

Press any key to continue . . .”

What can I do to solve the problem?

M. Sc. Ana Luísa Baddini
PHD student - Universidade Federal Fluminense- Niterói - Rio de Janeiro - Brasil

 

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Tomas Pluskal
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1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL:  +81-98-966-8684

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Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology

1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
TEL:  +81-98-966-8684

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