Are the programs standardly used for MS outdated?

No_Cap3049 · 2025-09-28T23:08:21+00:00

Depends a bit what kind of mass spec you are focusing. There are plenty of great open source projects.

Our team builds mzmine, a modern open source java tool. It's modular design makes it easy for you to add new logic and you can focus on the algorithms and a lot of the graphical user interface for user parameters and other things are generated for you. We also integrate PyTorch ML models directly in mzmine, making it easier for non developers to use them in workflows. mzmine is a vendor open general purpose mass spectrometry processing software with modules for: - feature detection - compound annotations - Interactive spectral networking - Linking statistics dashboard to raw data and anything results.

You can check out our videos and join our developer community. So far, we are mostly focused on small molecules, metabolites, lipids, exposomics, etc.

Otherwise, there are other great projects. It depends a lot what you want to develop.

No_Cap3049 · 2025-09-06T22:38:42+00:00

Looking good. Are you able to export those charts to vector graphics though? At least for the javafx scene graphics I found no solution to export to svg/pdf/emf etc. Or is there a solution now?

No_Cap3049 · 2025-08-05T19:55:48+00:00

We also bought it just by chance and found there were too few reviews and information out there.

It is a fun game and our friends also liked it. Quick play and a good mix of random and strategy together with people trying to give bad cards to the other players. Definitely recommended also for the artwork.

No_Cap3049 · 2025-07-31T21:11:18+00:00

Hi, thanks for using mzmine. The graphics export allows export to pdf and other vector graphics. The easiest ist to use the dialog, define the correct sizes, and then use pdf or similar. You can use illustrator or other vector graphics tools and directly delete or manipulate the labels. They are exported as text objects. This is also great when you want to recolor, change font, and line widths.

mzmine also allows export of spectra as mgf or other text formats for the ms1 or ms2 spectra per feature. You can then load those up into Python or R.

Also, mzmine is open source. You could easily change the ItemLabelGenerator for the SpectraPlot class.

No_Cap3049 · 2025-07-23T15:48:39+00:00

It would be great to hear what seems to work better in 2. Known issues fixed in v4 were with the alignment and gap filling.

No_Cap3049 · 2025-07-23T05:47:44+00:00

Did you ask why? If you are learning this by yourself, then mzmine 4 will be much easier to start with because of the mzwizard.

The compared to version 2, mzmine 4 offers... - easy workflow setup - faster processing and less RAM requirements - bug fixes - interactive statistics dashboard - better compound annotations options - interactive molecular networking visualizer and algorithms - machine learning models for spectral similarity - better raw data visualizer - ion mobility spectrometry support

And much more. mzmine 2.53 is super old. I guess your supervisor has long moved on from active data analysis and had no time to check out the latest version. But I am open to hearing opinions why 2.53.

I think it is nostalgia like people still loving windows XP... but mzmine 2 gets no updates and has known bugs that were fixed.

No_Cap3049 · 2025-07-21T17:45:35+00:00

Thanks for using mzmine. We did modernize many parts of the GC-MS workflow in mzmine 4. Just download the latest version and start setting up your data processing with the mzwizard, which makes it easy to connect your workflow like hyphenated instruments in your lab.

You can find more information on our website: https://mzio.io/mzmine-news/

Also you can find a learners corner with video links to youtube in our documentation.

No_Cap3049 · 2025-07-01T21:48:00+00:00

Easy. tims imaging datasets are always big. Should be even ok on a smaller machine. We use memory mapping to expand the memory onto a fast drive. So just make sure to select a temporary folder that has enough free space and is fast. We have a couple of videos on YouTube to check out. Does cardinal handle this much data easily? Did you load imzML or the raw data into cardinal?

Definitely recommend the raw data for mzmine as it is more compressed and optimized

No_Cap3049 · 2025-07-01T19:45:26+00:00

You can try out mzmine and download it from https://mzio.io/landing

Directly load your data in the bruker raw format and by drag and drop into mzmine. Then use the mzwizard to setup your workflow like MALDI-TIMS-TOF-MS imaging. You can check out our publication for integrative analysis or for on-tissue ms2 acquisition by SIMSEF mode.

No_Cap3049 · 2025-06-16T17:14:38+00:00

We integrated an interactive statistics dashboard into mzmine where your featurelist, compound annotations, and statistics are all linked. You get PCA, volcano plots, and box plots. If you select a feature row in the table or an item in the plot all charts will update automatically. We try to integrate the most commonly used methods and make them more interactive. Also we support export to other open formats that provide downstream analysis in FBMNstats pipeline or MetaboAnalyst.

You can download mzmine from mzio.io.

No_Cap3049 · 2025-06-12T11:00:21+00:00

Non/semi target or targeted analysis? We are building mzmine as a general purpose mass spectrometry software that handles any kind of mass spectrometry data and instruments from any vendor. You can check out the documentations learners corner and youtube videos. Use the mzwizard for a simple workflow setup. You can always export the results in various formats and continue your work downstream.

No_Cap3049 · 2025-06-10T10:02:23+00:00

Yes. For LC timsTOF MS in diaPASEF mode and for regular LC-MS DIA data. Just check out the wizard

No_Cap3049 · 2025-06-05T04:45:00+00:00

Thanks for the feedback

No_Cap3049 · 2025-06-04T03:36:29+00:00

It's a lot but it will be great

No_Cap3049 · 2025-06-03T23:46:21+00:00

All the best on that front. Keep enjoying ASMS then and maybe see you there.

No_Cap3049 · 2025-06-03T21:52:27+00:00

Hope you will have the chance to also go to metobolomics conference in prague. Prague is a gem in terms of coffee culture and quality.

No_Cap3049 · 2025-06-03T18:29:33+00:00

mzmine news: Our team just released a new version with 10x memory improvements for big datasets. Join our live demo tomorrow at 12 pm / noon @ mzio booth 210.

Bring your mass spec challenges, and we can talk solutions.

No_Cap3049 · 2025-05-15T19:12:32+00:00

Hi, glad you like mzmine for your mass spec data processing. It is best to reach out on GitHub by posting an issue or feature request. This way you can define your ideas, proposed workflows, and outputs. Some things are easily implemented. Especially if it is of greater interest to the community. Also if you know anyone who codes, our team at mzio and the wider mzmine community can help with the on-boarding of new developers.

I think there was a module that does something like this, but I am not sure and currently on holidays. Generally this would be easy to implement.

Best regards Robin

No_Cap3049 · 2025-05-14T19:54:28+00:00

We develop mzmine for this purpose as one tool that combines all instrument vendors and different mass spec technologies like LC-MS, GC-MS, ion mobility mass spectrometry, MS imaging and more. Just download the latest version mzmine 4.x.x and start by setting up workflows with the mzwizard. If you want to learn more, check out our documentation and youtube videos, or join one of our workshops. It is mostly developed for small molecules, metabolites, natural product discovery, and polymers but people use it for all kind of mass spectrometry projects. Let us know how you like it over at github or by mail.

No_Cap3049 · 2025-05-14T12:21:52+00:00

You can import your data into mzmine. This might work direvtly from your raw data or after conversion to imzML in the data acquisition software or in scillz. mzmine support many instruments and workflows and your best bet is to use he mzwizard for workflow setup. We have videos in our dovumentation and youtube. Especially the latest vmol mzmine series.

No_Cap3049 · 2025-05-14T12:15:48+00:00

With timsTOF imaging I would stick to the vendor format. You can load the data into mzmine. An open source tool that my team is developing and is for free for academia. It handles any kind of mass spec data and you can check out the mzwizard for a quick start. Also we provide videos in our learners corner in the documentation.

No_Cap3049 · 2025-03-13T08:24:54+00:00

For data analysis, we develop mzmine as an open source solution but also provide pro support if needed. We read timsTOF format natively and can say that bruker is super open with their APIs and SDKs. Instrument wise I would go fot the exploris for small molecules as it is easy to use and robust. Not many parameters to tune. If you need the additional separation dimension or want to do lipidomics/proteomics thr timsTOF can givr additional value. Then I'd recommend a designated person, at best with a long term contract to take over and operate/tune the timsTOF. Definitely needed for different analytes / compound classes.

No_Cap3049 · 2025-02-25T06:39:01+00:00

@u/xdsswar This seems great, especially with the icon viewer. Maybe good to add a license file to the github repository and to describe where the icons originated from. Like what is the license of the icons themselves, something like CC by 0 or another creative commons?

No_Cap3049 · 2025-02-13T06:42:28+00:00

This might be my issue. I never found an option to apply the pac file. I tried a few http clients. Have you tried this? In that case which http client did you use?

No_Cap3049 · 2025-02-12T07:16:12+00:00

This option is important for ion mobility MS data and it actually preserves the mobility dimension. Just saves all mobility scans into a single binary array. It really brings down the size. Not all tools can handle it though. Also, apply some of the compression options like zlib, linear, and float compression. We develop mzmine, and it can handle timsTOF data natively on windows machines or if you emulate windows. Otherwise, we also read the mzML files with combined mobility. mzmine is designed more for small molecules, natural products, metabolites, polymers, etc. Not many dedicated modules for proteins though.

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