MZmine error

[iñaki Lacomba]

Hello! I am trying to import my data to the program but it shows me an error, you can check it on the attached file. I have the Mzmine 2.53 version and 64 bits. 

Thank you for your help 

[Tomas Pluskal]

See https://github.com/mzmine/mzmine2/issues/697

Try to convert your data to mzML first.

Best regards,

Tomas

On Tue, Mar 3, 2020 at 3:20 AM iñaki Lacomba <inakil...@gmail.com> wrote:
>
> Hello! I am trying to import my data to the program but it shows me an error, you can check it on the attached file. I have the Mzmine 2.53 version and 64 bits.
>
> Thank you for your help
>

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[Geert Goeminne]

Hi, Sorry to reply here but i'm having troubles doing this on ithub so i gave up.

I jsut wanted to mention that in the latest version of MZmine it is not possible anymore to import Waters raw files, it does not recognize the files anymore and sees them as a folder. This makes it impossible to open any raw datafile from Masslynx.

Dragging the file into MZmine freezes the whole software.

Cheers, Geert

Geert Goeminne 

Head of VIB Metabolomics Core Ghent

https://corefacilities.vib.be/metabcore

VIB-UGent Center for Plant Systems Biology

Ghent University

Technologiepark 71 - 9052 Ghent - Belgium

Tel. +32(0)9 331 38 37

Skype: metacofa

www.psb.ugent.be

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[Tomas Pluskal]

Hi,

There is an issue on GitHub for this: https://github.com/mzmine/mzmine2/issues/774

Best,

Tomas

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[Geert Goeminne]

Thanks Tomas, did not see that. Problem is that i would like to export MSMS data to msp, and that is fixed in 2.53, maybe i should import the data in 2.52 and then proces in 2.53

When is Mzmine 3 expected?

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[Tomas Pluskal]

I guess I can make a bugfix release of 2.54. We made a great progress on version 3, but it will still take some time.

Tomas

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[Geert Goeminne]

Hi Tomas, oh, that would be very kind of you :)!

I'm for sure looking forward to MZmine 3, I understand this takes time, no worries!

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[Geert Goeminne]

Dear Tomas,

Hope you are fine!

Could you give an update on the potential release data of MZmine 3? Up to now we can still not upload Waters Masslynx RAW datafiles,which was possible in version 2.52.

You mentioned you would release a possible 2.54 version to fix that bug, but I have not seen any release anymore, possibly you want to move on with the 3.0 version instead of fixing the bug?

Any estimate on the release of version 3.0?

Thanks a lot for your reply,

Cheers, Geert

Due to COVID-19 safety measures that are currently effective, we offer limited services for urgent projects only until further notice. 

Geert Goeminne 

Head of VIB Metabolomics Core Ghent (MCG)

https://corefacilities.vib.be/metabcore

VIB-UGent Center for Plant Systems Biology

Ghent University

Technologiepark 71 - 9052 Ghent - Belgium

Tel. +32(0)9 331 38 37

Skype: metacofa

www.psb.ugent.be

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[Tomas Pluskal]

Hi Geert,

I have a position open for MZmine development: https://pluskal.group.uochb.cz/en/open-positions/80/phd-or-postdoctoral-position-in-computational-mass-spectrometry

If you know anyone who could be interested, please spread the word. 

I certainly want to release MZmine 3 this year, but also I have almost no time for coding these days, so that's the way things are.

Best regards,

Tomas

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[Geert Goeminne]

Dear Tomas,

Thanks for your reply, I asked around in my close environment but could not really find someone interested at this moment, but I will further spread the job announcement.

Looking forward to MZmine 3!

Stay safe,

Cheers, Geert

Due to COVID-19 safety measures that are currently still effective, some delays may occur, but don't look back 'cause we are not going that way.

Geert Goeminne 

Head of VIB Metabolomics Core Ghent (MCG)

https://corefacilities.vib.be/metabcore

VIB-UGent Center for Plant Systems Biology

Ghent University

Technologiepark 71 - 9052 Ghent - Belgium

Tel. +32(0)9 331 38 37

Skype: metacofa

www.psb.ugent.be

To view this discussion on the web visit https://groups.google.com/d/msgid/mzmine-devel/CAOH7_Hk_nwWKHugK33ySxZvv87N7r%3DqfvwYJ02mG0EVqKhF3_g%40mail.gmail.com.

[Geert Goeminne]

Dear,

I was wondering if there is any news on the release of MZmine 3? 

I understand that the release probably has not been realized last year, so I was wondering if there is any date set for the official release this year?

Thanks a lot for your response,

Cheers, Geert

Geert Goeminne 

Head of VIB Metabolomics Core Ghent (MCG)

https://connect.vib.be/cores/metabolomics-core-gent

VIB-UGent Center for Plant Systems Biology

Ghent University

Technologiepark 71 - 9052 Ghent - Belgium

Tel. +32(0)9 331 38 37

Mob. +32(0)479749971

Skype: metacofa

www.psb.ugent.be

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[Tomas Pluskal]

Hi Geert,

You can always download the latest development build from here: https://github.com/mzmine/mzmine3/releases

MZmine 3 is already pretty usable, I think. That said, it is not possible to give an exact date for the official release 3.0, we will likely try to time it according to the publication of a paper.

Best regards,

Tomas

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[Geert Goeminne]

Hi Tomas,

Thanks for the info.

Unfortunately while trying to import Waters Raw data I already get the following error:

I remember with the 2.53 version we had a similar problem with Waters Raw files, that's why we had to switch back to 2.52, and a 2.54 was never released.

Is this a general problem that has not been addressed yet or would the problem be on our side?

Cheers, Geert

 

Geert Goeminne 

Head of VIB Metabolomics Core Ghent (MCG)

https://connect.vib.be/cores/metabolomics-core-gent

VIB-UGent Center for Plant Systems Biology

Ghent University

Technologiepark 71 - 9052 Ghent - Belgium

Tel. +32(0)9 331 38 37

Mob. +32(0)479749971

Skype: metacofa

www.psb.ugent.be

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