Under the Microscope: MALDIBANK expands the potential of microbial identification

MALDI-TOF mass spectrometry has already transformed microbial identification, making it faster and more accessible in fields such as clinical microbiology. MALDIBANK, coordinated by MIRRI-ERIC, is taking the technology a step further: by bringing together a much broader diversity of microorganisms, richer reference data and advanced artificial intelligence, the project is opening new possibilities for identifying and profiling microbes across research, industry and environmental applications. 

MALDIBANK is a pioneering global initiative designed to change how we identify and profile microorganisms using MALDI-TOF mass spectrometry. This technology has demonstrated its reliability and is already widely used for microbial identification, particularly in clinical settings. However, its application remains largely limited to certain groups of microorganisms, such as bacteria and yeasts. 

 

How MALDIBANK makes a difference 

MALDI-TOF MS identification relies on comparing the mass spectrum of an unknown strain with reference spectra from microorganisms of known identity. MALDIBANK aims to unlock the full potential of this technology through two complementary approaches. Firstly, expanding the diversity and scope of reference databases by including a broader range of microorganisms (e.g. moulds, cyanobacteria, microalgae) and extending their application to new fields, such as agriculture, food and bioremediation. 

MALDIBANK is also leveraging AI models and advanced algorithms to extract additional information from MALDI-TOF MS profiles and develop new applications, such as toxicity assessment and antimicrobial resistance profiling. 

It is also worth noting that MALDIBANK is building an open-access and FAIR ecosystem for MALDI-TOF MS data and reference spectra. By making high-quality datasets and reference resources more accessible, interoperable and reusable, the project aims to overcome the fragmentation and limited availability that currently constrain the wider adoption and development of MALDI-TOF MS technologies. 

By combining broader microbial diversity, advanced data analysis, and open-access FAIR data resources, MALDIBANK seeks to move beyond simple microbial identification towards comprehensive microbial profiling, opening new possibilities for research, industry and environmental applications. 

 

From fungal identification to a global MALDI-TOF initiative 

The genesis of MALDIBANK lies in the collaboration between the BCCM/IHEM fungal collection (MIRRI-BE), hosted by Sciensano, and French partners from Sorbonne University and the Mycology & Parasitology Laboratory of La Pitié-Salpêtrière University Hospital (AP-HP, Paris). 

It all started with a simple observation: the identification of filamentous fungi (moulds) by MALDI-TOF MS in clinical settings was severely limited by the lack of comprehensive reference databases covering the diversity of fungal species. This diversity, however, was already represented in the BCCM/IHEM collection, which specialises in fungal pathogens. 

The strains preserved in the collection were therefore used to build an extensive repository of MALDI-TOF MS reference spectra for medically relevant fungi. In parallel, Sorbonne University and AP-HP developed MSI-2, a free, online identification platform that allows end users to upload their own MALDI-TOF MS spectra and identify their strains against the BCCM/IHEM reference database. 

A community of hundreds of users quickly formed around the platform, making MSI-2 a major success and demonstrating the strong demand for accessible MALDI-TOF MS-based identification tools. 

 

First results already taking shape 

Yet, much remained to be done. MALDIBANK acts as a catalyst, bringing together a unique network of partners with complementary expertise: culture collections with microbial resources and/or in-house MALDI-TOF MS databases (MIRRI-ERIC, EMBRC-ERIC, Westerdijk Institute), IT and AI experts (University of Turin, Sorbonne University, ELIXIR), as well as industrial partners. Together, they are building an open, cloud-based MALDI-TOF MS spectra database designed to enable both microorganism identification and comprehensive microbial profiling through advanced AI-driven analysis, while supporting the principles of Open Science and FAIR data. 

The initiative is complemented by a dedicated training program delivered in collaboration with INSTRUCT-ERIC, helping to build the skills and expertise needed to fully exploit the potential of this technology. 

After just one year, MALDIBANK has already delivered a first demo version of the platform, established a standardised framework for spectra and metadata collection, and launched its training program. 

 

Under the Microscope: the best way to keep on track of MIRRI-ERIC  

Every first Friday of each month, MIRRI-ERIC releases a news article from the series "Under the Microscope", showcasing key developments, from funded research projects to collaboration opportunities and milestones across our network. Stay tuned!

 

This text was prepared in collaboration with Pierre Becker (BCCM/IHEM, Sciensano, MIRRI-BE).