An international team of scientists led by Tomáš Pluskal from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) has introduced a new generation of software enabling scientists to analyze large volumes of data from mass spectrometry, a technique that separates chemicals by their weights. The open-source project MZmine provides a new window into the chemical space that surrounds us and lives within. The latest advances in <a href="http://mzmine.github.io/">MZmine 3</a> are now published in a <a href="https://www.nature.com/articles/s41587-023-01690-2">Nature Biotechnology</a> paper.
<h3>Challenges of biochemical analysis</h3>
Analytical chemists of the world, unite! This paraphrase could characterize the joint efforts of scientists across the globe, who, using the methods of mass spectrometry, strive to decipher and analyze the chemical composition of complex samples from various origins, especially in biological and clinical studies. Each individual sample can contain hundreds of thousands of different chemical compounds that scientists need to trace, quantify, and identify to understand their impact on human health or their ecological role.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Robin_Schmid_Pocet_spustni_modulu_M_Zmine_v_letech_2017_2022_152c3eae85/UOCHB-Robin-Schmid-Pocet-spustni-modulu-MZmine-v-letech-2017-2022.jpg" alt="IOCB Prague/Robin Schmid: MZmine module runs in 2017–2022 (in millions)"/>
Even relatively small studies result in gigabytes of ‘raw’ data to be processed and interpreted. It is the processing, analysis, and comparison of a multitude of molecular data that constitutes some of the most challenging steps in biochemical analysis today. This is also a major bottleneck that limits the ability of scientists to expand knowledge and come up with exciting new discoveries.
<h3>Community-driven development</h3>
For this reason, a group of international scientists started in 2005 to develop the open-source software MZmine to aid the analysis of mass spectrometry data. The community developing this software has been co-established by Czech scientist <a href="https://pluskal.group.uochb.cz/en">Tomáš Pluskal</a>, who has been coordinating the project almost since its inception and is currently a group leader at IOCB Prague.
“The greatest strength of the MZmine project is the international community of experts that has formed around the project. At conferences, presentations on MZmine are always well received,” says Tomáš Pluskal about the project.
Robin Schmid from IOCB Prague and UC San Diego (CA, USA), one of the first authors of the paper, adds: “It&#39;s fantastic when we meet researchers from other countries for the first time and they tell us that MZmine and our support has saved their PhD thesis or projects. That&#39;s the best appreciation one can hope for.”
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Tomas_Bellon_Tomas_Pluskal_vlevo_a_Robin_Schmid_oba_z_UOCHB_92138f0c1d/UOCHB-Tomas-Bellon-Tomas-Pluskal-(vlevo)-a-Robin-Schmid-(oba-z-UOCHB).jpg" alt="IOCB Prague/Tomáš Belloň: Tomáš Pluskal (left) and Robin Schmid (both from IOCB Prague)"/>
The first version of MZmine has enabled scientists to automate the processing of datasets generated by analytical devices at an unprecedented scale. The second generation of MZmine, released in 2010, made the project more widely known and led to the formation of a worldwide community of researchers using the software and continuing to expand its functions with additional modules and applications. The publication introducing the second generation of MZmine has since collected more than 2,200 citations in scientific articles and the tool itself has been used to process millions of different measurements.
<h3>Third generation</h3>
The newest MZmine 3 brings several major improvements. Whereas the previous version allowed scientists to analyze hundreds of samples in a matter of days, the new generation makes it possible to process thousands of samples per hour. Besides vastly accelerating data processing, the new version of the software can also be used, for the first time, to link different data types, especially time-resolved and imaging data.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Nature_Biotechnology_M_Zmine_open_source_komunitni_projekt_pro_integrativni_zpracovani_dat_LC_IMS_MS_a_IMS_MS_6d9b3759d1/UOCHB-Nature-Biotechnology-MZmine-open-source-komunitni-projekt-pro-integrativni-zpracovani-dat-LC-IMS-MS-a-IMS-MS.jpg" alt="IOCB PRague/Nature Biotechnology: MZmine, an open-source community project for integrative LC–IMS–MS and IMS–MS data processing"/>
This opens up opportunities for researchers to more easily analyze and interpret complex biological samples. MZmine is a tool to investigate the causes and mechanisms of diseases, detecting useful clinical biomarkers for diagnostics and identifying chemicals in the environment. This includes previously unknown chemical structures, which might prove valuable for the discovery and development of new drugs for medical applications.
The third generation of MZmine was announced in a paper prepared, besides Tomáš Pluskal as the corresponding author, by the first authors Robin Schmid (IOCB Prague and UC San Diego), and Steffen Heuckeroth and Ansgar Korf (both from University of Münster, Germany), joined by over three dozen other contributors from around the world.
“MZmine has established itself as a trusted tool for mass spectrometry researchers over the past decade. Its modular framework has fostered community participation in the development of the MZmine code, leading to significant advancements featured in the newly released MZmine 3,” says Ansgar Korf of University of Münster.
The development of the MZmine project has been supported by the Czech Science Foundation (project No. 21-11563M).
<ul>
<li>Literature for using the MZmine software <a href="https://lcms.labrulez.com/library?search=MZmine">in the LabRulezLCMS library</a></li>
<li>Literature for using the MZmine software <a href="https://gcms.labrulez.com/library?search=MZmine">in the LabRulezGCMS library</a></li>
</ul>

A breakthrough in big data processing helps trace chemicals in complex mixtures

<a href="https://icpms.labrulez.com/products/1086">USP-ID</a>, delivered by <a href="https://icpms.labrulez.com/companies/298">Mestrelab Research</a>, makes powerful qNMR analysis easy. This software allows lab scientists to identify chemicals and impurities quickly. Beyond automatic identification, quantification, and labeling, USP-ID improves spectral interpretability with quantum-mechanical models based on USP reference standards and smart analytics. USP-ID also resolves overlapping peaks, even when no single signal is distinct. 
Michael Levy, SVP of Digital &amp; Innovation at USP, said: “Mestrelab’s delivery of USP-ID within Mnova brings this powerful software to a valuable network of analytical chemistry customers. The joint solution makes qNMR analysis more accessible to all. We are excited to unlock the value provided by this partnership.” 
Santiago Dominguez, CEO of Mestrelab, said: “NMR is a unique analytical technique from the perspective of the richness of information it provides and, with its evolution towards benchtop instruments, it has the potential to deploy in many use cases beyond its traditional research applications. USP-ID is an extremely powerful technology which turns benchtop NMR into an accessible technique for quality control and mixture analysis applications. We are very excited by this integration with Mnova, which enhances the power and applicability of our tools and opens new markets and solves difficult to tackle problems and look forward to continue to develop what we see as a strategic partnership with USP.”
To learn more about USP-ID, delivered by Mestrelab, and to add USP-ID as an application within Mnova, please visit <a href="http://www2.mestrelab.com/l/271522/2024-03-25/3nwsnf">mestrelab.com/software/usp-id/</a> or <a href="https://www.usp.org/products/qnmr-mestrelab">usp.org/products/qnmr-mestrelab</a>.
*The integration of USP-ID into Mnova does not imply approval, endorsement, or certification by USP of Mestrelab products, nor does it imply that Mnova is necessarily the best available product for the purpose or that any other brand or product was judged to be unsatisfactory or inadequate. As a standard setting organization, USP avoids conflicts of interest that interfere or appear to interfere with its impartiality and objectivity.
<blockquote>
About USP
</blockquote>
<blockquote>
USP is an independent, scientific nonprofit organization focused on building trust in the supply of safe, quality medicines. For over 200 years, USP has worked to build trust where it matters most: in the world&#39;s medicines, dietary supplements, and foods. While USP’s public health mission has remained unchanged for over 200 years, the global healthcare landscape has been anything but static. Advances in analytical methods, manufacturing processes, and digital innovations are changing the science of how medicine quality is assessed and maintained. USP’s portfolio of solutions addresses quality assurance, builds a stronger medicines supply chain, enhances regulatory predictability, and helps manufacturers distribute quality medicines, dietary supplements, and foods.
</blockquote>
<blockquote>
About Mestrelab
</blockquote>
<blockquote>
MESTRELAB RESEARCH, with nearly two decades of expertise, specializes in advanced analytical chemistry solutions. Our comprehensive toolset supports pharmaceutical and biopharmaceutical industries, addressing Research and Development (R&amp;D) and Quality Control (QC) needs, including NMR, LC/GC-MS, and optical spectroscopy data analysis. Committed to streamlining workflows and automating processes, we empower customers to prioritize scientific innovation over routine tasks. Collaborating closely with industry leaders, we take pride in creating cutting-edge tools seamlessly integrated into workflows, ensuring an efficient experience for our valued customers. 
</blockquote>

The U.S. Pharmacopeia (USP) and Mestrelab Research, S.L. (Mestrelab), are pleased to announce they have entered into a collaboration to deliver USP-ID, through Mestrelab’s Mnova platform.

The TRILAB DeltiQ 2, 3D printer from the Brno-Hradec Králové company TRILAB is a high-quality 3D printer from the so-called pro-sumer segment of the desktop 3D printer category. It is a printer completely developed by TRILAB, designed and built only from high-end components. Its hardware and software is adapted and tuned for short, but also multi-day prints even without the presence of an operator. Thanks to the remote-control software and the built-in camera with lighting, the user is constantly in control of printing. Also in the case of ambiguity, question or problem, the printer is immediately remotely diagnosed by the TRILAB service team.
Thanks to the technical and application support of the TRILAB team and also thanks to the many years of experience of the two main partners of TRILAB in the field of science and research, where Dr. Vojtěch Tambor is originally the leading researcher in the laboratory of the Center for Biomedical Research (CBV) of the University Hospital HK and Dr. Michal Boháč is a former director of Bruker s.r.o., every scientific customer is always perfectly professionally secured and can thus focus only on solving their own challenges and projects.
Thanks to practical experience with placing 3D printers in research laboratories, TRILAB also knows very well that the DeltiQ 3D printer does not only allow its owners to save time and money in producing things that are familiar and hard to reach, but also and above all to create and quickly test completely new things, not yet discovered. In addition, it allows them to be pampered by the quality of the printing surface, spatial accuracy, huge print volumes or even just the grace of delta kinematics movements. In addition, the customer does not have to buy the printer as an investment, but can rent it or cleverly buy it under an initial operating lease with a possible subsequent purchase. This not only divides the financial costs of its acquisition over a longer period, but also avoids possible lengthy approval processes for investment purchases.
The DeltiQ 3D printer will become a great help in your research project. Whether it&#39;s simple holders or specialized components, with a 3D printer you can save not only most acquisition costs, but also a lot of time spent looking for a suitable tool. In addition, you can create tools that you cannot buy as they do not exist! And besides tools, you can also create your own prototypes, products or their models and replacements.
<h3>The story of <a href="https://www.nenovision.com/">NenoVision</a>: Thanks to 3D printing, our microscope can be touched safely</h3>
NenoVision is a start-up originating from the Central European Institute of Technology CEITEC and is one of the incubated companies in the South Moravian Innovation Center JIC INMEC. They are proud that their LiteScope microscope is the only one in the world that can combine data from an electron microscope and an atomic force microscope in detail and assemble them into 3D models. It literally opens up a new dimension of research.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Trilab_Neno_Vision_mikroskop_1_6b79421014/Trilab-NenoVision-mikroskop-1.jpg" alt="TRILAB: NenoVision - model of LiteScope microscope printed on the TRILAB DeltiQ printer"/>
The company found the application of 3D printing in solving the problem of how to enable the &quot;touch&quot; of the microscope to partners, customers and the professional public: &quot;LiteScope normally works in a controlled environment, moreover in a vacuum, and it is a sensitive and very expensive device. Therefore we or our distributors cannot normally carry it to all events and exhibitions, nor provide it to our partners for tests for insertion into their machines,” explains Jan Neumann, the owner and CEO of NenoVision.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Trilab_Neno_Vision_mikroskop_2_8d96758735/Trilab-NenoVision-mikroskop-2.jpg" alt="TRILAB: NenoVision - model of LiteScope microscope printed on the TRILAB DeltiQ printer"/>
Machining the individual components of the microscope itself is so expensive that even making a copy of the instrument without &quot;living&quot; components does not make sense. In the end, 3D printing proved to be an elegant solution: “Since the complete 3D model for production was already ready, it was enough to prepare and print it on a TRILAB DeltiQ printer and the model of the device in perfect quality and accuracy was born. In this way, it can be easily reproduced and shown to customers and the public at a fraction of the normal cost,” adds Jan Neumann. 
<h3><a href="https://www.biocev.eu/en">BIOCEV</a> story: Own online nanospray built in a few days?</h3>
The story of <a href="http://peterslab.org">Dr. Petr Novák</a> from BIOCEV shows the second group of 3D printing options. Building something that does not exist, that you cannot buy, and you know what it should look like and you need it. Dr. Novák&#39;s team happened to be in exactly the same situation. Commercially available nanosprays did not meet the requirements not only in terms of compatibility with available spectrometers, but also in terms of real sensitivity, essential for measurement. That&#39;s why the &quot;Do it yourself&quot; mode came into play. Thanks to the clever use of 3D printing, a nanospray was created, which has ncomparably higher sensitivity and operator comfort compared to all commercial devices available on the market. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Trilab_BIOCEV_online_nanosprej_1_ac1e93326c/Trilab-BIOCEV-online-nanosprej-1.jpg" alt="TriLab: BIOCEV - online nanospray"/>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Trilab_BIOCEV_online_nanosprej_2_ba9dbfde99/Trilab-BIOCEV-online-nanosprej-2.jpg" alt="TriLab: BIOCEV - online nanospray"/>
<h3>The story of the MALDI-TOF plate suitable not only for affinity chromatography</h3>
As part of the projects of AffiPro, a spin-off company under BIOCEV Prague, it has been running for several years under the leadership of Dr. Petr Novák and Dr. Petr Pompach for the development of clinical applications of affinity chromatography on MALDI-TOF spectrometry, for example MALDI Biotyper devices, by patented application of various antibodies to MALDI plates using the so-called soft ion landing technology. Although this is a technology that is just beginning and commercial use is yet to come, they already have several very interesting surfaces on their own chips in the laboratory, which will be interesting in the future not only for clinical and veterinary, but also for military screening. And thanks to the use of 3D printing technology, they have the opportunity to print not only different surfaces and shapes, but also to use different materials on MALDI chips and thus, for example, increase the sensitivity and detection limits of the method. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Trilab_Affi_Pro_MALDI_TOF_desticka_836e1e69b7/Trilab-AffiPro-MALDI-TOF-desticka.png" alt="TriLab: AffiPro/BIOCEV - MALDI-TOF chip for affinity chromatography"/>
The original article <a href="https://pubs.acs.org/doi/pdf/10.1021/acs.analchem.0c01737">Three-Dimensional Printed Target Plates for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry ke stažení.</a>

TRILAB 3D printing solutions and DeltiQ 2 printers are in the lab at home

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The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) is a leading scientific institution in the Czech Republic, recognized internationally. Its primary mission is basic research in the fields of chemical biology and medicinal chemistry, organic and material oriented chemistry, chemistry of natural compounds, biochemistry and molecular biology, physical chemistry, theoretical chemistry, and analytical chemistry. 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

SciY, a vendor-agnostic Bruker BioSpin division, drives R&D and manufacturing digitalization and automation. Its harmonized solutions cover experiment design, data management, analysis, automation, and AI readiness, empowering next-generation self-driving labs and factories.

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