MZmine 3 beta released

[Robin Schmid]

To the MZmine community,

We are happy to announce the first MZmine 3 open beta release. A lot of work went into improving all aspects of MZmine - delivering a new graphical user interface and enhanced processing options. Some key features include better memory management and a fully multi-threaded workflow solving bottlenecks in sample alignment (join aligner) and gap-filling. Testing MZmine 3 on various complex LC-MS/MS datasets with ~1000 samples, processing only required 1-2 h on a regular data analysis computer, including feature finding, alignment, and data export.

Download the latest stable release:
https://github.com/mzmine/mzmine3/releases/tag/v3.0.0-beta

or the latest development build:
https://github.com/mzmine/mzmine3/releases/

Retweet our message:
https://twitter.com/mzmine_project/status/1498974133371215878?s=20&t=y-EDbshvjR8IyMI-42QAsQ

For users:
Double click on a raw data file to explore data. For a quick start into MZmine, the new Batch wizard helps set up a standard LC-MS/MS processing workflow.

For macOS:
Currently, MZmine 3 lacks a signature for macOS. However, while we are working on this, users can allow MZmine in the macOS Gatekeeper protection by running the following command in the terminal from the folder containing the .app.

sudo xattr -cr MZmine.app
For developers:
In case you want to include your development in MZmine 3 or if your tool depends on MZmine outputs, check out our codebase on GitHub:
https://github.com/mzmine/mzmine3

Community contact:
Join our slack community:
https://join.slack.com/t/mzmine/shared_invite/zt-151egtpww-gXA9DR3OvaAIrewHYawhUQ

And join our weekly MZmine web café to discuss issues and ideas with the developers or other community members. The next meeting is scheduled for next week:
Wednesday, 9th March, 5 pm CET/8 am PST
https://ucsd.zoom.us/j/96822012735 
and will be joined by Tomas Pluskal, Steffen Heuckeroth, Ansgar Korf, Daniel Petras, Robin Schmid, and more.


Best regards,

The MZmine core team

[Geert Goeminne]

DearRobin,

Thanks for the update,

But i have reported this already a few times, it is impossible to open Waters Raw data files since version 2.53, I was hoping this would be solved now but it is still not possible. The problem is, when you go to a Masslynx folder, with previous versions (2.52 and earlier), MZmine was recognizing that the Masslynx project was containing the RAW files, but now it forces you to go to the RAW folder itself, and then gives you the following error:

How can we open Waters RAW files without the need for converting them first to mzML?

Thanks a lot,

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,

The Waters import module doesn't get much of our love, since we use Thermo and Bruker instruments. But anyway, we are working on a new Waters module that will also support ion mobility data. You just need to wait a bit more.

Best regards,

Tomas

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[Geert Goeminne]

Dear Tomas,

Ok, understood :) Will wait for an update then, and for now work with mzML converted files from Waters Masslynx RAW data. 

Do you mean with the new module also Unifi .uep files would be enabled to import? I hate that data format, it's horrible (Oracle database structure), unfortunately this is the only platform our Vion system (which can only be controlled by UNIFI) works with.

Nice job on the MZmine 3 version by the way!

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,

I am not familiar with the .uep format. Is that a newer or older format than MassLynx .raw? We want to use the data access library provided by Waters, so whether we can read .uep depends on whether the library supports it. In any case, it would be great if you could share a few .uep files with us for testing.

Best regards,

Tomas

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[Robin Schmid]

Hey Geert,

sorry that this took so long. We were more occupied with other parts of MZmine and I think that converting any kind of data to mzML is usually the best idea. Also for data sharing.
I looked at the problem today and was able to fix it for some test .raw files that I found online. Could you test this version (scroll down; might need a github account to see the artifacts):
https://github.com/mzmine/mzmine3/actions/runs/1953947966

Select the Waters RAW import and either select the .RAW folder or better, the direct parent folder.

Hopefully, this fixes the problem. As Tomas said we are trying to get a student to implement the native library support for IMS data.

Best regards,

Robin

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[Geert Goeminne]

Hi Robin,

Thanks for the update. I realize mzML is the best way to go, but of course this is all data duplication, and mass specs do already produce a lot of data, so we try to avoid duplicating large datasets.

I can see the Artifacts, but i can't donwload the installer, do i need a github login to be able to download?

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[Geert Goeminne]

Hi Tomas,

.uep is the extension of Unifi, a lot of Waters systems run on UNIFI since the release 5 years ago.

.eup contains all information of a project, the raw data, the processed data, but also instrument method. Everything is Oracle database, you can't see the separate files within a .uep file. There is a way though to convert the data with Proteowizard to mzML format, but the Proteowizard needs to connect to the Waters Database on the local computer, which requires specific computer settings to enable access. So I think it will be impossible to access .uep files with MZmine unless you set up this connection.

This also means that .uep files are quite large because they contain the whole dataset, I could send you a small dataset but it's already 1GB, I sent you a link through WETRANSFER.

Let me know if you were able to download the data please.

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[Tomas Pluskal]

Hi Geert,

I got the uep file and I uploaded it into our repository of sample datasets for testing: https://drive.google.com/open?id=1gsqml4Vo8z4-O04_zsLaS3JC_0hqZfAj

Best regards,

Tomas

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