LC-MS/MS Laboratory


The LC-MS/MS laboratory contains the following cutting-edge equipment:-

Agilent Technologies 6520 Accurate Mass Q-TOF LC/MS

This system is capable of providing a better mass accuracy – more than 2-ppm for MS and more than 5-ppm for MS/MS. It has a broad mass range and high mass resolving power of up to 20000.

The Q-TOF system can be set up in several configurations to support different research needs:-

  1. Integrated with nanoflow LC system and HPLC-Chip/MS interface to provide a highly sensitive analytical technique for the identification of peptides at high-femtogram to low-picogram level.
  2. Integrated with Agilent 1290 UHPLC and Dual-ESI source for metabolomic studies or natural product analysis.
  3. Coupled with AP-MALDI PDF+ source

Main Applications:

  • Perform accurate molecular weight measurement.
  • Identification of unknown compounds, which include small molecule, peptides or proteins.
  • Quantitative proteomic studies with isobaric tags or isotope coded affinity tags.

Agilent Technologies 6410 Triple Quad LC/MS

This system is capable of providing femtogram-level limit of detection and quantification. The QQQ system can be configured with Agilent 1200 HPLC or Agilent 1290 UHPLC to cater for different research needs.

  • Available scan modes: MS scan, MS/MS product ion scan, MRM, DMRM, MS/MS neutral loss and gain scan, precursor ion scan, SIM.
  • Available Ionization source: ESI
  • Main Applications: To perform screening, confirmation and quantification on known small molecule compounds or proteomics samples.


MassHunter Softwares

MassHunter Workstation Acquisition Software

This is used to tune the mass spectrometer, control and monitor instrument parameters, set up methods containing acquisition parameters and worklist containing multiple samples.
MassHunter Workstation Qualitative Analysis Software.

MH Qual allows user to extract and integrate chromatograms, extract peak spectra and compare data from different types of data files. More importantly it contains feature to find compounds and generate formulas for those compounds.

MassHunter Workstation Quantitative Analysis Software

This software is used to set up a batch of data files, quantify and evaluate the results.

MassHunter Workstation METLIN Metabolite PCD/PCDL

  • PCD is an accurate mass compound database.
  • PCDL contains both an accurate mass compound database and an MS/MS accurate mass spectral database, which is often referred to as a spectral library.
  • METLIN PCD (Personal Compound Database) and PCDL (Personal Compound Database and Library) is one of the best-known and most-comprehensive metabolite databases. It includes annotated list of over 24,000 endogenous and exogenous metabolites, as well as di- and tripeptides. Each entry may include mass, chemical formula, and structure information, as well as ID numbers that link to more information about the compound, such as the CAS and ChemSpider IDs.

Agilent Mass Profiler Professional (MPP)

MPP is a powerful statistical analysis and visualization tools designed for use with mass spectrometry data in metabolomics and proteomics studies.

The main functions include:-

  • Perform MS-based differential analysis. To determine relationship among two or more sample groups.
  • Provides comprehensive statistical tools including ANOVA, PCA, volcano plots, hierarchical trees, SOMs, QT clustering, and five different methods for class prediction.
  • Generates inclusion list for subsequent MS/MS-based analyses to facilitate identification of compounds of interest.
  • Recursive Analysis
  • The ID Browser allows integrated identification and annotation of compound using LC/MS Personal Compound Databases.
  • Pathway Analysis suite

MassHunter BioConfirm Software

Bioconfirm software is used together with qualitative analysis software to analyze both protein and peptide spectra using separate, optimized deconvolution algorithms. It is ideally suited for users who need to support recombinant protein expression and process development, known-protein characterization, or synthetic peptide confirmation.

MassHunter Workstation Optimizer Software

This automated MS method development software helps in optimizing the data acquisition parameters for MRM mode on a QQQ mass spectrometer for each individual compound analyzed. Specifically, it automates the selection of the best precursor ions, the optimization of the fragmentor voltage for each precursor ion, selection of the best product ions, and optimization of collision energy value for each transition for a list of compounds.

Spectrum Mill

Spectrum Mill software is a collection of tools for high throughput processing of MS and MS/MS spectra to provide protein and peptide identifications and relative quantitation. The main functions include:-

  • Spectral preprocessing for MS/MS and MS-only data, including spectral quality filtering and precursor charge state assignment for MS/MS spectra.
  • Protein database search
  • Data review, validation and comparison of large data sets
  • De novo sequencing
  • Identification of mutations, post-translational modifications and chemical modifications.
  • Differential expression quantitation

PEAKS Studio 6.0 Proteomic Mass Spectrometry Software

PEAKS is an integrated software platform for several common proteomics analysis using tandem mass spectrometry data. The main functions include:-

  • Peptide de novo sequencing
  • Peptide / protein identification with database search
  • Post-translational modification analysis
  • Homology analysis
  • Protein quantification – PEAKS Q


Services Overview


Peptides and Protein Identification
* Identification of in-gel / in-solution digested protein    
* Intact molecular weight determination for peptides and proteins

* Quantitative study on ICAT, iTRAQ or other isobaric labeled samples.
* Peptide Quantification

Simple C4/C18 sample desalting with ZipTip

Small Molecule

→ Accurate mass analysis and identification of small molecule
→ Quantitative measurements of small molecules

Contact for Service

Staff in-charge

Contact details

Tel: +603 5514 4405
Fax:+603 5514 6323
Office : Room 3-2-46\


Jeffery Cheah School of Medicine and Health Sciences
Monash University Malaysia
LC-MS/MS Laboratory (Room: 3-2-46)
Building 3, Level 2, Room 46,
Jalan Lagoon Selatan,
46150, Bandar Sunway,
Selangor Darul Ehsan,Malaysia.

Download LCMS sample submission forms below:-