LC-MS/MS Laboratory


The LCMS/MS Platfrom currently consist of four LCMSMS instruments which are:

  • Agilent 6550B iFunnel Q-TOF
  • Agilent 6520B Q-TOF
  • Agilent 6410B Triple Quadrupole
  • Agilent 6495C Triple Quadrupole

The Agilent 6550 iFunnel Quadrupole Time-of-Flight (Q-TOF) mass spectrometer delivers the lowest detection levels of any high resolution LC/MS instrument. By incorporating with Agilent Jet Stream technology and dual-stage ion funnel, the system is able to achieve a 10-fold increase in sensitivity for selected molecules as compared to an earlier generation Q-TOF. In combination with ChipCube interface, the robust Agilent 6550 i-Funnel Q-TOF system is specifically set to processed protein/peptide samples derived from various backgrounds such as plant, snake venom, microorganisms which includes viruses, bacteria and fungi, blood plasma and serum and so forth, yet still manage to give reproducible results. Despite being set to process protein/peptide samples, the system is configuration is interchangeable according to the desired setup for analysing various types of samples in order to meet the ever increasing demands from clients.


The Agilent 6520 Q-TOF delivers exceptional analytical performance for MS and MS/MS analyses for experiments demanding the highest accurate-mass measurements. These improvements enable scientists in metabolomics, proteomics and complex qualitative analyses to find and identify more compounds faster than ever. All of this performance is achieved without significantly compromising rapid analysis time for higher-quality data. The Agilent 6520 Q-TOF features attomole sensitivity, better than 2-ppm MS mass accuracy approaching FTMS mass accuracy, better than 5-ppm MS/MS mass accuracy -much better than FTMS mass accuracy at fast spectral acquisition rate, tenfold improvement in in-spectra dynamic range without loss of sensitivity, mass resolution to 20,000 not dependent on spectral acquisition rate, fast data acquisition compatible with fast LC chromatography and broad mass range from m/z 50 to 3200. Although it can carry out other type of analysis, this system is mainly specialised in compound discovery.


The Agilent 6410 Triple Quadrupole LC/MS System is the proven choice for your quantitative applications in pharmaceutical ADME/DMPK studies, biomarker validation, clinical research, food safety, forensics, toxicology, and environmental analyses. The system meet quantitative needs with triple quadrupole performance which gives superior sensitivity, renowned performance reliability, and easy upgradeability. The 6410 Triple Quad features MS/MS sensitivity and repeatability multiple scan modes namely MS scan, MS2 scan, product ion scan, MRM, MS/MS neutral loss/gain scan and precursor ion scan among all.


The Agilent 6495C Triple Quadrupole LC/MS is the latest quantitative solution introduced by Agilent Technologies. With similar, yet improved features with the 6410 Triple Quad, the 6495C Triple Quad is more sensitive, have higher accuracy and resolution, which makes it a great choice to quantify isomers.



There are three main softwares used in the LCMS/MS lab, namely the Agilent Masshunter Series, SpectrumMill and PEAKS X.


  • MassHunter Workstation Acquisition Software
    • To acquire data during sample analysis/run
  • SpectrumMill
    • Spectrum Mill is a proteomics workbench, which process MS and MS/MS data to provide protein/peptide identification and relative quantification. It is a collection of tools for high throughput processing of MS and MS/MS spectra to provide protein and peptide identifications and relative quantitation.
    • PEAKS X (PEAKS 10) is another software package for proteomics mass spectrometry data analysis offered in our lab. PEAKS X is well recognized for its accuracy in de novo sequencing. This software shares two similarities with SpectrumMill, namely for protein/peptide identification and non-labelled quantification (relative quantification).
    • Apart from these similarities, PEAKS X provides other parameters that makes it a comprehensive software for protein studies.
  • MassHunter Workstation Quantitative Analysis Software
    • For absolute quantification of targeted protein.


  • MassHunter Workstation Acquisition Software
    • To acquire data during sample analysis/run
  • MassHunter Workstation Qualitative Analysis Software
    • Main software for metabolomic analysis where it is use for compound identification, paired with the validated Metlin Database.
  • MassHunter BioConfirm Software
    • For intact mass analysis on intact protein sample.
  • MassHunter Workstation Quantitative Analysis Software
    • For absolute quantification of targeted compound.

Industrial Partner

Monash University Malaysia have signed a Memorandum of Understanding with Agilent Technologies Sales (Malaysia) Sdn Bhd on the 2nd December 2019. It was the third MoU signed to enhance the relationship between Monash and Agilent and also for the placement of Agilent's 129 Infinity II UHPLC 6495C QQQ mass spectrometer for a period of 12 months. This was held after the two MoUs that were previously signed in 2011 and 2016

Services Overview


  • Digested protein/peptide identification
  • Non-labelled quantification of protein/peptide (relative quantification)
  • Labelled relative quantification (example, iTRAQ)
  • Intact protein analysis (mass determination)
  • Absolute quantification (determination of concentration of targeted protein)\
  • Sample desalting (post-digestion cleanup)
  • Pre and post-analysis consultations.


  • Accurate mass analysis
  • Compound identification and compound confirmation.
  • Absolute quantification (determination of concentration of targeted compound)
  • Pre and post-analysis consultations.

Contact us

For pricing and further inquiries, please contact:


LCMS Platform, Room 3246, Building 3,
Level 2. Jeffrey Cheah School of Medicine and Health Sciences,
Monash University Malaysia, Jalan Lagoon Selatan,
47500 Bandar Sunway, Selangor.

Download LCMS sample submission forms below:-