Mass Spectrometry Platform

IMB Mass Spectrometry Platform

IMB’s Mass Spectrometry Platform is home to a comprehensive suite of state-of-the-art mass spectrometry, high-performance liquid chromatography, and robotic instrumentation. The facility has been continually refined and expanded to support high-throughput, qualitative and quantitative investigation of complex biological systems.

The platform enables researchers at IMB to address a wide range of mass spectrometry applications, including molecular discovery, identification, characterisation, and quantification. These capabilities support insights into protein structure and interactions, amino acid sequencing, post-translational modifications, compound stability, and the bioavailability of potential therapeutics across diverse biological systems.

Recent discoveries enabled by the facility include the identification and characterisation of novel therapeutic candidates from natural product extracts using de novo peptide sequencing, as well as quantitative studies of bioavailability supporting drug discovery pipelines targeting chronic pain, breast and ovarian cancer, and chronic kidney disease.

Mass Spectrometry Instrumentation

The platform hosts a diverse and complementary fleet of mass spectrometers spanning discovery, quantitative, and structural workflows:

• ZenoTOF 7600 – next-generation high-sensitivity TOF platform enabling enhanced depth in proteomics and low-abundance detection

  • Intabio ZT system – advanced platform for protein characterisation and charge variant analysis

• 6600 TripleTOF systems (x3)– flagship high-resolution instruments for proteomics, metabolomics, lipidomics, and SWATH/data-independent acquisition workflows

• 5600 TripleTOF system – high-resolution discovery instrument supporting proteomics, PTM analysis, and metabolomics

• 5800 MALDI TOF/TOF systems (×2) – high-throughput proteomics and structural characterisation using high-energy MS/MS

• 4000 QTRAP systems (×2) – highly sensitive hybrid triple quadrupole/ion trap instruments for targeted quantification and structural analysis

• Triple Quad 4500 – robust quantitative platform for targeted assays and biomarker validation

• API 4000 and API 3200 mass spectrometers – reliable triple quadrupole systems for routine quantitative workflows

Capabilities

These instruments collectively provide:

• High-resolution accurate mass analysis (ppm-level accuracy)

• Fast MS and MS/MS acquisition (up to 100 scans/sec on TOF systems)

• Data-independent acquisition (SWATH) and MS/MS All workflows

• Targeted quantification (MRM, SRM, HRSRM)

• De novo peptide sequencing and database-driven protein identification

• Post-translational modification analysis (phosphorylation, glycosylation, etc.)

• Proteomics, metabolomics, and lipidomics workflows

• Structural elucidation of small molecules and biomolecules

• High-throughput sample analysis and protein quantification

Separation, Robotics, and Automation

• Integrated nanoLC, capillary LC, and UHPLC systems for high-sensitivity separations

• Automated HPLC–MALDI workflows using Shimadzu, Probot, and Agilent robotic platforms

• High-throughput sample handling and preparation pipelines

Bioinformatics and Data Analysis

• ProteinPilot (v4.5–5.0)

• Mascot

• PEAKS Studio

• Open-source mass spectrometry analysis tools

The platform currently assists over 150 different users from various institutions and fields. They have come to rely on IMB’s expertise and knowledge in both molecular science of natural products, and of the hardware and software of the various instruments at their disposal.

Our platform provides technical advice, research and training support, and can assist in the various stages of research, from concept through to experimental approach, including design, methodology, data acquisition and data processing, and project reporting and publication.