The Mass Spectrometry Technology Section offers a range of techniques for identification, characterization and quantification of proteins, peptides and metabolites. The facility is equipped with a high-resolution mass spectrometer and advanced data analysis software.


Protein Digestion

  •   Protein has to be cut enzymatically into smaller peptides before the LCMS/MS analysis.

  •  Mixture of Trypsin-LysC enzyme is used to digest the protein.

  • The digestion process can be performed either in-solution or in-gel.

Protein Identification

  • Digested peptides are analysed using the on-line reversed phase nanoLC coupled with Orbitrap Fusion.

  •  The data analysis software is used to search the acquired MS/MS spectra to identify the proteins. The software will confirm the identified protein and the post-translational modifications if present.

Relative Protein Quantification

  • Proteins expression in difference samples treatment can be compared relatively using an isotope labeling or label-free approach.

  • The data analysis software is used to generate a peak area (intensity) of identified protein for a statistical analysis.

De Novo Peptide Sequencing

  • Peptide of interest in the range of 10-15 amino acids can be sequenced using mass spectrometer.

  • Sequencing service includes pre-acquisition prior to mass spectrometer and possible sequence will be confirmed by fragmentation data (MS/MS).


The Metabolomic service is equipped with a single quadrupole detector mass spectrometry coupled with UHPLC to separate and detect a targeted molecular mass. This equipment is an easy way to generate an extra dimension of information from your separation. The sample also can be direct injected into the mass spectrometry for getting fast result of molecular mass. There are the services that we offer:

  •   Analysis of known compound or targeted compounds based on molecular mass

  • Nominal mass determination.

  •  Peak purity and impurity profiling.

  • Syntheses confirmation.

  •  Increase success of identify peak of interest based on mass.

  • Quantitative Analysis.

  • Direct Infuse Mass Spectrometry (DIMS).

Key Instrumentation

–  nanoLC coupled with Orbitrap Fusion (LCMS/MS)
–  UHPLC coupled with Single Quadrupole Detector (SQD)


        Proteome Discoverer for Identification & Quantification Analysis

        MarkerLynx and MetaboLynx for Metabolite & Biomarker Analysis

        DeNovoGUI for De Novo peptide sequencing

        QuanLynx for Quantitative Analysis

  • Discussion – Strategy & Exchange, Project Design Objective, Type of Sample Extractions, Method QC data output
  • Send Request Form / Sample / Submission Form / PO
  • Sample QC – Quality Assessment, Concentration, Quality & Quantity
  • Performing Run On The Instrument – Proteins/Metabolic Compounds are run on respective instruments according to service needs.
  • Raw Data Analysis – Raw data reports will be analysed by the specific analysis software according to project objective.
  • Data Delivery – Raw data and reports will be sent by email. Printed copies are available upon request. Raw data will be delivered in HDD drive.