Equipment

The Proteomics and Metabolomics Platform currently consist of six instruments:

• Agilent 6550B iFunnel Q-TOF
• Agilent 6520B Q-TOF
• Agilent Atomic Absorption Spectrophotometer (Agilent AAS 240 Duo system)
• Agilent 1200 and 1260 HPLC
• ProteinSimple Jess Automated Western Blot System
• AKTA Prime Plus- Fast Protein Liquid Chromatography System

Agilent 6550B iFunnel Q-TOF

The Agilent 6550 iFunnel Quadrupole Time-of-Flight (Q-TOF) mass spectrometer delivers the lowest detection levels of any high-resolution LC/MS instrument. Incorporating Agilent Jet Stream technology and dual-stage ion funnel, the system achieves a 10-fold increase in sensitivity compared to earlier-generation Q-TOFs. Combined with the Agilent 1290 UHPLC, this robust system processes protein/peptide samples from diverse backgrounds, such as plants, snake venom, microorganisms (viruses, bacteria, fungi), blood plasma, and serum, while maintaining high reproducibility. Its configuration is adaptable for various sample analyses to meet increasing client demands.

Agilent 6520B Q-TOF

The Agilent 6520 Q-TOF delivers exceptional analytical performance for MS and MS/MS analyses, providing highly accurate mass measurements. Its features include attomole sensitivity, better than 2-ppm MS mass accuracy, and fast spectral acquisition rates, enabling advanced metabolomics, proteomics, and complex qualitative analyses. With a broad mass range (m/z 50–3200) and compatibility with fast LC chromatography, this system excels in compound discovery while maintaining rapid analysis times.

Agilent Atomic Absorption Spectrophotometer (Agilent AAS 240 Duo system)

The Agilent AAS 240 Duo system combines flame and graphite furnace capabilities to provide versatile, high-performance atomic absorption spectroscopy. It is used to quantify trace metals and elements in biological, environmental, and industrial samples. This system is well-suited for analyzing trace metal levels in proteomic and metabolomic studies, providing accuracy and reliability in element detection.

Agilent 1200 and 1260 HPLC

The Agilent 1200 and 1260 HPLC systems are versatile platforms for high-performance liquid chromatography. They deliver precise separations and reproducible results for a wide range of samples, including complex proteomic and metabolomic mixtures. These systems are equipped to handle high-throughput workflows, supporting both qualitative and quantitative analyses.

ProteinSimple Jess Automated Western Blot System

The Jess system revolutionizes traditional Western blotting with its fully automated platform, enabling high-sensitivity protein quantification and size separation in a fraction of the time. This system provides reproducible, quantitative data for complex protein analyses, making it invaluable for studying post-translational modifications and protein expression profiles in proteomics.

AKTA Prime Plus- Fast Protein Liquid Chromatography System

The AKTA Prime Plus is a fast protein liquid chromatography (FPLC) system designed for protein purification, fractionation, and characterization. Its versatility allows it to handle a variety of biomolecules, from antibodies and enzymes to venom proteins. This system is essential for sample preparation in proteomics workflows, ensuring high-purity outputs for downstream analyses.

Software

The Proteomics and Metabolomics Platform utilizes the following softwares for data analysis:

Proteomics

• MassHunter Workstation Acquisition Software
  • Used for data acquisition during sample analysis or runs.
• PEAKS Software (Peaks X+ and Peaks 12.5)
  • Renowned for its accuracy in de novo sequencing, PEAKS is a powerful software package for proteomics mass spectrometry data analysis.
  • It supports protein/peptide identification and label-free quantification (relative quantification), similar to SpectrumMill.
  • Additionally, PEAKS offers advanced features that make it a comprehensive tool for protein studies.
• MassHunter Workstation Quantitative Analysis Software
  • Used for the absolute quantification of targeted proteins.
• Other Proteomics Tools
  • Free software such as Skyline, FragPipe and SpectrumMill is also available for specific analyses and workflows.

Metabolomics

• MassHunter Workstation Acquisition Software
  • Used for data acquisition during sample analysis or runs.
• MassHunter Workstation Qualitative Analysis Software
  • Primary software for metabolomic analysis, enabling compound identification when paired with the validated Metlin Database.
• MassHunter BioConfirm Software
  • Designed for intact mass analysis of protein samples.
• MassHunter Workstation Quantitative Analysis Software
  • Used for the absolute quantification of targeted compounds.

Industrial Partner

Monash University Malaysia has maintained a longstanding strategic partnership with Agilent Technologies, formalised through a Memorandum of Understanding (MOU) in 2022. This collaboration initially led to the establishment of the Agilent Integrated Biology Facility @ Monash Malaysia (AIBF). In 2025, the partnership was expanded and rebranded as the MUMPMP–Agilent BioDiscovery Hub, aligning it more closely with the Monash University Malaysia Proteomics and Metabolomics Platform (MUMPMP) and the University’s broader research and translational agenda.

The BioDiscovery Hub houses a comprehensive suite of state-of-the-art analytical instruments, including the Agilent Revident QTOF LC-MS system coupled with the Agilent 1290 Infinity III UHPLC and the Agilent 5977 GC-MSD. These advanced platforms support cutting-edge research in proteomics, metabolomics, lipidomics, and related multi-omics applications. The Hub operates as a shared, open-access research facility, enabling collaborative projects and service provision for Monash Malaysia staff and students, as well as external academic, clinical, and industry partners.

Services Overview

Proteomics

• Protein/Peptide Identification: Identification of digested proteins and peptides using advanced mass spectrometry techniques.
• Label-Free Quantification: Relative quantification of proteins/peptides without labeling.
• Sample Desalting: Post-digestion cleanup to ensure sample quality before analysis
• Consultations: Pre- and post-analysis consultations to discuss experimental design, data interpretation, and troubleshooting.

Metabolomics

• Accurate Mass Analysis: Precise mass measurement for metabolite characterization.
• Compound Identification and Confirmation: Comprehensive compound profiling and validation using validated databases.
• Consultations: Pre- and post-analysis consultations to guide study design and data interpretation.

Download Proteomics and Metabolomics Platform eFlyer here

Download Agilent Integrated Biology Facility eFlyer here

Request for services on Proteomics and Metabolomics Platform iLab

Publications and Acknowledgements

Your use of the Monash Malaysia Research Infrastructure is heavily subsidised by the University. To comply with internal reporting obligations, the platform must report on the number and type of publications produced by users of the platform/ facility. It is essential that we have this information so that we can continue to provide the advanced instrumentation, staff, training and assistance that you and other researchers require to undertake your work.

It is a condition of use of platform that:
1. You acknowledge the platform and any significant assistance provided by the staff members in your publications;
2. Platform staff members who made a significant scholarly contribution should be co-authors on the publication, in accordance with Monash’s Research Authorship And Attribution Policy, see Research Authorship and Attribution Policy.

Please acknowledge MUMPMP in your publications by including:
"The authors acknowledge the use of instruments and scientific and technical assistance at the Monash Malaysia Proteomics and Metabolomics Platform (MUMPMP)”.
Or,
if the work was carried out with help from MUMPMP staff (but not enough to justify coauthorship):
"The authors acknowledge the use of instruments and scientific and technical assistance of Name of PMP Staff Member at the Monash Malaysia Proteomics and Metabolomics Platform (MUMPMP).”

Please always notify the relevant platform when acknowledgment is made.

Location

Email

mum-pmp@monash.edu

Contact