We recently tried MZmine and the feature finder seems to work well :)
We mainly use Agilent’s Mass Profiler since it works with our instrument and if anyone goes that way we have finally figured out good feature finding parameters ;)
We mainly use Agilent’s Mass Profiler since it works with our instrument and if anyone goes that way we have finally figured out good feature finding parameters ;)
December 12, 2024 at 1:39 AM
We recently tried MZmine and the feature finder seems to work well :)
We mainly use Agilent’s Mass Profiler since it works with our instrument and if anyone goes that way we have finally figured out good feature finding parameters ;)
We mainly use Agilent’s Mass Profiler since it works with our instrument and if anyone goes that way we have finally figured out good feature finding parameters ;)
Today @ansgarkorf.bsky.social is presenting a brand new compatibility, matching the best in class #mzmine software with the brand new #timsMetabo platform.
Come and speak to him at poster 464 for find out how you can discover MoRE! #ASMS2025
Come and speak to him at poster 464 for find out how you can discover MoRE! #ASMS2025
June 5, 2025 at 2:21 PM
Today @ansgarkorf.bsky.social is presenting a brand new compatibility, matching the best in class #mzmine software with the brand new #timsMetabo platform.
Come and speak to him at poster 464 for find out how you can discover MoRE! #ASMS2025
Come and speak to him at poster 464 for find out how you can discover MoRE! #ASMS2025
I would bet on MZmine for performance (I keep postponing getting to it). But the biggest challenge might be the learning curve and requirement of scripting to combine output with IDs (e.g. proteomics applications).
December 11, 2024 at 11:30 AM
I would bet on MZmine for performance (I keep postponing getting to it). But the biggest challenge might be the learning curve and requirement of scripting to combine output with IDs (e.g. proteomics applications).
To visualize properly in mzmine
December 18, 2024 at 8:50 PM
To visualize properly in mzmine
You don't have to redistribute the dlls with mzmine. Leave it to the users. You already request users to install pwiz to convert raw data, and that comes with acceptance of vendors' licensing terms. Just look for the class and, if available, call it. Seems legit to me.
May 15, 2025 at 9:33 AM
You don't have to redistribute the dlls with mzmine. Leave it to the users. You already request users to install pwiz to convert raw data, and that comes with acceptance of vendors' licensing terms. Just look for the class and, if available, call it. Seems legit to me.
New article on natural product discovery uses the #mzmine molecular networking workflow. The authors deposited their data in the public domain and added the mzmine batch configuration file for reproducible #MassSpec data processing:
biotechnologyforbiofuels.biomedcentral.com/articles/10....
biotechnologyforbiofuels.biomedcentral.com/articles/10....
Discovery of the antifungal compound ilicicolin K through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei - Biotechnology for Biofuels and Bioproducts
Background Given the global rise in antimicrobial resistance, the discovery of novel antimicrobial agents and production processes thereof are of utmost importance. To this end we have activated the g...
biotechnologyforbiofuels.biomedcentral.com
March 17, 2025 at 4:03 PM
New article on natural product discovery uses the #mzmine molecular networking workflow. The authors deposited their data in the public domain and added the mzmine batch configuration file for reproducible #MassSpec data processing:
biotechnologyforbiofuels.biomedcentral.com/articles/10....
biotechnologyforbiofuels.biomedcentral.com/articles/10....
We run ~100 rich samples in mzmine even with 16GB ram at a reasonable time. MZmine has some nice optimization hints for large datasets. mzmine.github.io/mzmine_docum...
Performance options - mzmine documentation
mzmine.github.io
December 19, 2024 at 7:37 AM
We run ~100 rich samples in mzmine even with 16GB ram at a reasonable time. MZmine has some nice optimization hints for large datasets. mzmine.github.io/mzmine_docum...
Authors published a paper in Biorxiv, they used MZmine in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
www.biorxiv.org
September 6, 2025 at 12:00 PM
Authors published a paper in Biorxiv, they used MZmine in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
Only a few days remain to register for the first official mzmine Community Meeting, taking place on April 28-29 at @iocbprague.bsky.social.
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
March 11, 2025 at 3:22 PM
Only a few days remain to register for the first official mzmine Community Meeting, taking place on April 28-29 at @iocbprague.bsky.social.
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
In case that is still relevant: There was an issue in older mzmine versions that caused merged spectra (created during library matching) to not be saved properly. The issue is resolved for projects created in mzmine 4.4 and higher.
January 22, 2025 at 3:35 PM
In case that is still relevant: There was an issue in older mzmine versions that caused merged spectra (created during library matching) to not be saved properly. The issue is resolved for projects created in mzmine 4.4 and higher.
mzmine webinar series in collaboration with VMOL. This series will focus on various aspects of mass spectrometry data processing, showcasing the capabilities of mzmine.
Sign up for free!
Sign up for free!
October 21, 2024 at 7:32 AM
mzmine webinar series in collaboration with VMOL. This series will focus on various aspects of mass spectrometry data processing, showcasing the capabilities of mzmine.
Sign up for free!
Sign up for free!
Next Tuesday, Nov 19, 5 pm CET / 8 am PST we will have the next #VMOL seminar #mzmine series on multimodal data processing using mzwizard.
And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0
And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0
November 14, 2024 at 7:50 PM
Next Tuesday, Nov 19, 5 pm CET / 8 am PST we will have the next #VMOL seminar #mzmine series on multimodal data processing using mzwizard.
And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0
And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0
"You will be visited by three spirits"...
Meanwhile, the three spirits:
#metabolomics #TeamMassSpec #chemsky
Meanwhile, the three spirits:
#metabolomics #TeamMassSpec #chemsky
December 25, 2024 at 8:46 AM
Workshop "MS-based #metabolomics for #cyanobacteria metabolites", during #ICTC13 (4 May 25). Speakers: @daniel-petras.bsky.social, @siliakop.bsky.social
Free with a student registration in ICTC13.
@func-metabo-lab.bsky.social @gnps2.bsky.social #MZmine #GNPS2 #TeamMassSpec
More: www.ictc13.gr
Free with a student registration in ICTC13.
@func-metabo-lab.bsky.social @gnps2.bsky.social #MZmine #GNPS2 #TeamMassSpec
More: www.ictc13.gr
November 27, 2024 at 5:37 AM
Workshop "MS-based #metabolomics for #cyanobacteria metabolites", during #ICTC13 (4 May 25). Speakers: @daniel-petras.bsky.social, @siliakop.bsky.social
Free with a student registration in ICTC13.
@func-metabo-lab.bsky.social @gnps2.bsky.social #MZmine #GNPS2 #TeamMassSpec
More: www.ictc13.gr
Free with a student registration in ICTC13.
@func-metabo-lab.bsky.social @gnps2.bsky.social #MZmine #GNPS2 #TeamMassSpec
More: www.ictc13.gr
Thank you, MZmine Team! Yes, when I started using MZmine 4.4.3, this issue has been fixed. Whenever I open a previously saved project, it loads the correct spectral library annotations. Thank you!
January 24, 2025 at 11:13 PM
Thank you, MZmine Team! Yes, when I started using MZmine 4.4.3, this issue has been fixed. Whenever I open a previously saved project, it loads the correct spectral library annotations. Thank you!
Random selection from Pastel's #proteomics resources page http://bit.ly/1J4g3CE - = - http://mzmine.github... | Mzmine | MS data processing with main focus on LC-MS data
---
#proteomics #prot-other
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#proteomics #prot-other
November 7, 2023 at 9:03 AM
Random selection from Pastel's #proteomics resources page http://bit.ly/1J4g3CE - = - http://mzmine.github... | Mzmine | MS data processing with main focus on LC-MS data
---
#proteomics #prot-other
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#proteomics #prot-other
Please file a new issue here: github.com/mzmine/mzmin...
Issues · mzmine/mzmine
mzmine source code repository. Contribute to mzmine/mzmine development by creating an account on GitHub.
github.com
January 6, 2025 at 8:24 PM
Please file a new issue here: github.com/mzmine/mzmin...
Only used it for small molecule and imaging datasets so far: mzmine mzio.io It reads timstof files natively and is super fast compared to data analysis.
mzio – Accelerate Scientific Discoveries
mzio.io
July 23, 2025 at 6:28 AM
Only used it for small molecule and imaging datasets so far: mzmine mzio.io It reads timstof files natively and is super fast compared to data analysis.
In case you missed part 2 of our our #mzmine seminar series on @ansgarkorf.bsky.social on:
- LC-MS²
- GC/EI-MS
- MALDI imaging
the recording is online here:
www.youtube.com/watch?v=cGA5...
Coming up next:
Dec 3rd, 5 PM CET / 8 AM PST
@steffenheu.bsky.social on analyzing LC-MS and LC-IMS-MS data
- LC-MS²
- GC/EI-MS
- MALDI imaging
the recording is online here:
www.youtube.com/watch?v=cGA5...
Coming up next:
Dec 3rd, 5 PM CET / 8 AM PST
@steffenheu.bsky.social on analyzing LC-MS and LC-IMS-MS data
VMOL Seminar #29 - mzmine series: 2. Multimodal Data Processing (Ansgar Korf)
YouTube video by Functional Metabolomics Lab
www.youtube.com
November 25, 2024 at 4:36 PM
In case you missed part 2 of our our #mzmine seminar series on @ansgarkorf.bsky.social on:
- LC-MS²
- GC/EI-MS
- MALDI imaging
the recording is online here:
www.youtube.com/watch?v=cGA5...
Coming up next:
Dec 3rd, 5 PM CET / 8 AM PST
@steffenheu.bsky.social on analyzing LC-MS and LC-IMS-MS data
- LC-MS²
- GC/EI-MS
- MALDI imaging
the recording is online here:
www.youtube.com/watch?v=cGA5...
Coming up next:
Dec 3rd, 5 PM CET / 8 AM PST
@steffenheu.bsky.social on analyzing LC-MS and LC-IMS-MS data
#research #MassSpectrometry #metabolomics #lipidomics #bioinformatics
Reproducible mass spectrometry data processing and compound annotation in MZmine 3: doi.org/10.1038/s415...
Reproducible mass spectrometry data processing and compound annotation in MZmine 3: doi.org/10.1038/s415...
May 27, 2024 at 9:04 AM
#research #MassSpectrometry #metabolomics #lipidomics #bioinformatics
Reproducible mass spectrometry data processing and compound annotation in MZmine 3: doi.org/10.1038/s415...
Reproducible mass spectrometry data processing and compound annotation in MZmine 3: doi.org/10.1038/s415...
Is there anyone comfortable using mzmine potentially able to help me figure out what I'm doing? (GC-EI-MS...) Thanks in advance! @mzmine.bsky.social
June 20, 2025 at 7:25 PM
Is there anyone comfortable using mzmine potentially able to help me figure out what I'm doing? (GC-EI-MS...) Thanks in advance! @mzmine.bsky.social
Authors published a paper in #BioRxiv, they used MZmine in the study. Including #RRIDs will make this less ambiguous.
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
Sending mixed signals: convergent iridescence and divergent chemical signals in sympatric sister-species of Amazonian butterflies
www.biorxiv.org
February 13, 2025 at 1:01 PM
Authors published a paper in #BioRxiv, they used MZmine in the study. Including #RRIDs will make this less ambiguous.
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
SciScore.com made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #RRID #reproducibility
Indeed @angelsi.bsky.social used a supercomputer and 1584 Go ram for 500 samples to align them etc...with mzmine
December 19, 2024 at 5:51 AM
Indeed @angelsi.bsky.social used a supercomputer and 1584 Go ram for 500 samples to align them etc...with mzmine
Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine #AC pubs.acs.org/doi/10.1021/...
Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine
Lipid A, a crucial component of lipopolysaccharides (LPS), plays a pivotal role in the pathogenesis of Gram-negative bacteria. Lipid A patterns are recognized by mammals and can induce immunostimulato...
pubs.acs.org
April 1, 2025 at 8:01 PM
Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine #AC pubs.acs.org/doi/10.1021/...