Microcystins (MC) are a critical class of toxic cyanobacterial secondary metabolites, with specific variants such as MC-LR strictly regulated in drinking water. Despite their extensive structural dive...

Microcystins (MC) are a critical class of toxic cyanobacterial secondary metabolites, with specific variants such as MC-LR strictly regulated in drinking water. Despite their extensive structural diversity, comprising over 300 known congeners, comprehensive environmental monitoring is severely hindered by the limited availability of commercial reference standards and public tandem mass spectrometry (MS/MS) spectra. To address this analytical bottleneck, we developed a non-targeted mass spectrometry-based computational workflow leveraging the Mass Spectrometry Query Language (MassQL) to enable comprehensive MC profiling. By systematically analyzing the chemical space and fragmentation patterns of all MC congeners documented in the CyanoMetDB database, we classified the congeners into nine structurally distinct groups. Subsequently, we designed and optimized a suite of MassQL queries targeting the conserved MC backbone, group-specific motifs, and individual constituent amino acids. The performance of these custom queries was rigorously evaluated following Feature-Based Molecular Networking (FBMN). Application across three independent cyanobacterial bloom datasets comprising both in-house and public data acquired via qTOF and Orbitrap high-resolution mass spectrometry platforms demonstrated highly satisfactory analytical performance based on recall, precision, F1-scores, and Matthews Correlation Coefficients (MCC). We further demonstrated that MassQL functions as a powerful MC candidate prioritization tool orthogonal to molecular networking. By interrogating MS/MS data for specific structural motifs, this query-based approach enabled the discovery and annotation of novel MC congeners lacking public library spectra, significantly enhancing non-targeted screening for water quality and risk assessment.

The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills.

The Mass Query Language (MassQL) enables scientists to precisely express and reproducibly search for mass spectrometry (MS) peak patterns in large MS datasets. MassQL has been adopted across the most ...

The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and ex...

An advanced metabolomic workflow featuring expert knowledge-tailored mass spectral queries and multi-informative molecular networking was applied to French DNA-barcoded collections of Amanita species ...

With over 3000 representatives, the monoterpene indole alkaloids (MIAs) class is among the most diverse families of plant natural products. The MS/MS spectral space exploration of these complex compou...

The Mass Query Language (MassQL) enables scientists to precisely express and reproducibly search for mass spectrometry (MS) peak patterns in large MS datasets. MassQL has been adopted across the most ...

The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is in...

Nature Methods - The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of...

MassQL is empowering scientists to uncover hidden environmental pollutants and toxins — without writing a single line of code.

The Mass Query Language (MassQL) enables scientists to precisely express and reproducibly search for mass spectrometry (MS) peak patterns in large MS datasets. MassQL has been adopted across the most ...

Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...

Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and ...