Hi Angela,
> I have some problems using MzMine 2.10 version for processing my data. Below
> I will describe you my case:
>
> My data:
>
> Mzmine version 2.10
> Operating systems information: 64 bit; installed memory (RAM) 8.00 GB ;
> processor intel (R) Core (TM, i7-3770S CPU).
> Windows edition Windows 7 Professional.
> Java SE runtime Environment 8 (jre-8-windows-x64.exe).
> I've only changed the Heap Size at 7830 MB, according to my computer
> performance.
> I worked on a LC-ESI(orbitrap)Mass Spectrometer so I have high resolution
> files (132 raw files thermo) in MS1 level (Xcalibur version 2.1.1).
> Starting processing by MZMine 2.10:
>
> First step: import files, no problem for all 132 files!
> Second step: data set filtering: Crop Filter (retention time 10 to 26 min) no
> problems for all 132 files!
> Third step: mass detection: centroid (selected noise level 5000) no problems
> for all 132 files!
> Fouth step: chromatogram builder: min time span 0.0, min heigh 5000; m/z
> tolerance 0.2 m/z or 20 ppm. This process is very slow but the most important
> thing is that after processing the first 40 files a task error concerning
> with a problem with the heap size of Java appears.
By setting the "min time span" to 0.0 you are telling MZmine to track
information about all ions, even if they appear only in a single scan. That's
why you run out of memory. Try setting the "min time span" to a more reasonable
value, according to the length of your chromatographic peaks. And read the
manual carefully :)
> I' ve also tried using the targeted peak detection by importing a csv file
> (see attached file cacao.csv) (intensity tolerance 10%; m/z tolerance 0.2 m/z
> or 20 ppm,; retention time tolerance 2.0 absolute min) but every time i try
> to apply these parameters to my raw thermo files a task error telling that my
> files could not be read or they are empty appears...but of course this is not
> true because I can see their content!
To check this you need to send me a sample data file.
Best regards,
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
WWW: https://groups.oist.jp/g0
TEL: +81-98-966-8684
Fax: +81-98-966-2890
------------------------------------------------------------------------------
Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment
Start a new project now. Try Jenkins in the cloud.
http://p.sf.net/sfu/13600_Cloudbees
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
