Dear Thomas,
I can't send you my project file due to confidentiality issues. However,
based on what you said, I think I have found the correct parameters as I
was being too stringent before.
Thanks for pointing me in the right direction!
Sincerely
Cynthia Roy
Étudiante au doctorat
945 av. Wolfe | 4e étage | Québec, QC, G1V 5B3
Tel (418) 650-5115 Extension 4633
Tomas Pluskal <plus...@oist.jp>
15/10/2014 20:37
Veuillez répondre à
Developer discussion <mzmine-devel@lists.sourceforge.net>
A
Developer discussion <mzmine-devel@lists.sourceforge.net>
cc
"cynthia....@inspq.qc.ca" <cynthia....@inspq.qc.ca>
Objet
Re: [Mzmine-devel] Deconvolution
Hi Cynthia,
The answer is: yes you can, at least in majority of the cases.
The "baseline cut-off" deconvolution module is not very practical, though.
It is meant only as a proof-of-concept method for demonstration purposes.
I suggest using the "local minima search". If you send me your MZmine
project file, I can assist you with optimizing the parameter values.
Cheers,
Tomas
On Oct 16, 2014, at 5:06, cynthia....@inspq.qc.ca wrote:
Dear Thomas,
Here it goes:
1. I am currently using a 64-bit OS computer, Java Version 7 update 60,
MZmine 2, R version 3.1.1.
2. HEAP_SIZE=1024
R_HOME=C:\Users\roycyn01\Documents\R\R-3.1.1
I have modified R_HOME to suit my location and the HEAP_SIZE was
originally 2048.
3. - No problems related with R
4. I have been following the workflow proposed in the User Manual
- Crop filter for the time and masses
- Baseline Correction
- Mass detection
- Chromatogram builder
- Deconvolution (Which is my question, how to deconvolute 2 isomers not
totally separated)
5.
Here we achieved successful deconvolution of the 2 isomers but at the
expense of our lower intensity ions (around 1.0E3)
So my question here is : Can we successfully deconvolute those 2 isomers
without loosing the integration of our lower intensity ions in the
process?
Thank you
Cynthia Roy
Étudiante au doctorat
945 av. Wolfe | 4e étage | Québec, QC, G1V 5B3
Tel (418) 650-5115 Extension 4633
Tomas Pluskal <plus...@oist.jp>
14/10/2014 20:35
Veuillez répondre à
Developer discussion <mzmine-devel@lists.sourceforge.net>
A
Developer discussion <mzmine-devel@lists.sourceforge.net>
cc
"cynthia....@inspq.qc.ca" <cynthia....@inspq.qc.ca>
Objet
Re: [Mzmine-devel] Deconvolution
Dear Cynthia,
It should be possible, but you have to provide more details. Ideally,
please send an example data file so we can take a look at it. Please
follow the 'How to report problems' section of the MZmine 2 manual.
Best regards,
Tomas
On Oct 15, 2014, at 0:38, cynthia....@inspq.qc.ca wrote:
> Dear developpers,
>
> We are currently processing LC-MS data in an untargeted fashion. We have
2 isomers of interest not completely separated (around 60%) and were
wondering if there is a way to deconvolute the 2 isomers without loosing
the small intensity peaks of the rest of the run.
>
> Thank you
>
> Cynthia Roy
> Étudiante au doctorat
> 945 av. Wolfe | 4e étage | Québec, QC, G1V 5B3
> Tel (418) 650-5115 Extension 4633
>
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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
<MZMine - Deconvolution
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===============================================
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
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