About This Facility

The mass spectrometry (MS) resources on campus aim to provide researchers with state-of-the-art techniques and equipment to characterize biomolecules including proteins and peptides (Proteomics), glycans and their conjugates (Glycomics & glycoproteomics), metabolites (Metabolomics) and lipids (Lipidomics). A number of state-of-the-art instruments for the separation, identification and quantitation of all major biomolecules by mass spectrometry based approaches are available. In addition to providing MS based structural characterization services, the mass spectrometry facility on the Bangalore Life Science Cluster campus provides training to on-campus students, postdocs and researchers on the use of different LC-MS/MS technologies as well as develop new analytical methods required to be on cutting-edge and to facilitate on-campus research.

There are four MS units operate under the facility to be able to provide expertise training and services in each of the different ‘-omics’ platforms.

1) Proteomics

2) Small molecule Mass spectrometry

MS facility is driven to establish a hyphenated Mass Spectrometry based small molecule analysis  platform in basic biology, clinical studies and biotechnology at Bangalore Life Sciences Cluster (BLiSc) affiliated institutes; NCBS, CCAMP and InStem. The platform undertakes clinical, biological, chemical, ecology studies of lipidomics/ metabolites for BLiSc community and external researchers. Direct infusion as well as LC-MS/MS methods using HRMS like Orbitrap technology (Orbitrap Fusion, Q-Exactive, Orbitrap XL) are available.

Identification and quantification of known and unknown Proteins/ Peptides Lipids/metabolites in biological fluids such as plasma, urine, saliva and tissue using Data dependant (DDA) and data independent (DIA) analysis for the estimation of lipids and other metabolites. Comprehensive lipid profiling and quantitation is a system-based study of all possible lipid classes in the biological system. Phosphoinositides measurements in cell signaling.

Instruments

InStem Mass spec facility for Qualitiative and Quantitative charactetization of Biomolecules

Zeno TOF 7600 – Zeno TOF 7600 is coupled high flow UPLC for analysis of metabolite, Protein, Peptide and Lipids. The 7600 Zeno TOF having the power of Zeno trap in combination with the binary fragmention mechnism i.e. Collision induced dissociaton and EAD ( Electron activated dissociation) is very useful for the characterization of biomolecules. The high resolution of the analyzer is well suited for the characterization of biosimilars, Biobetter and intact proteins. Due to zeno trapping of the ion the sensitivity of this platfrom is enhanced multiple fold and dynamic range for the quantitation has also got improved significantly.

Following Mass Spectrometry Platfroms are present in the BLiSc cluster institutes.

• Thermo Q-Exactive
• 5600 Triple TOF with Capillary LC and Conventional UPLC
• TSQ Vantage-Agilent 1290 UHPLC (LC-MS)
• Thermo Orbitrap Fusion with Easy Nano LC II
• Sciex QTRAP 6500 MS/MS with Shimadzu UPLC
• Sciex QTRAP 5500 MS/MS with Shimadzu UPLC
• Thermo LTQ XL with Waters UPLC
• Thermo Fleet
• GCMS single Quad
• GCMS Triple Quad

Instruments for Proteomics / Protein Characterization / Targeted Metabolomics / Untargeted Metabolomcis / HRMS

Thermo Q-Exactive

The combination of LC separation, high resolution MS and MS2 analysis should provide unambiguous and precise characterization of different classes of lipids in biological samples. Q-Exactive MS with its mass resolution of 140,000 at 400 m/z and mass accuracy of 1-2 ppm is optimized for lipidomics and metabolomics experiments. HCD fragmentation using stepped normalised collision energies is an excellent tool for identification and quantitation of different classes of lipids.

SCIEX QTRAP 6500 MS/MS

The Sciex QTRAP 6500 builds on the capabilities of the 5500 series with improved sensitivity and linear dynamic range. One of the best is class triple-quadrupole MS instrument for the targeted quantitative analysis with MS3 fragemntation that enable for identification. It features the advanced IonDrive technology, which increases ion production & transmission efficiency. It also equipped with the differnetial ion-mobility technology.

Thermo Orbitrap Fusion with Easy Nano LC II

The Orbitrap Fusion is a state-of-the-art hybrid mass spectrometer that integrates quadrupole, linear ion trap, and Orbitrap mass analyzers. It offers unparalleled flexibility and performance, with ultra-high resolution and accurate mass measurements. This instrument excels in deep proteome analysis, post-translational modification studies, and high-throughput screening, providing comprehensive data for complex biological research.

Sciex QTRAP 5500 MS/MS

The Sciex QTRAP 5500 is a triple quadrupole linear ion trap mass spectrometer known for its high sensitivity and fast scanning capabilities. It combines quantitative and qualitative analysis in a single run, making it a powerful tool for biomarker discovery, drug metabolism, and protein identification. Its advanced features enhance accuracy and reduce analysis time, improving overall workflow efficiency.

Thermo LTQ Orbitrap XL

LTQ Orbitrap XL MS with its mass resolution of 140,000 at 400 m/z and mass accuracy of 1-2 ppm is optimized for lipidomics and metabolomics experiments. The combination of LC separation, high resolution MS and MS2 analysis provides unambiguous characterization of different classes of lipids in biological samples. CID fragmentation using pulsed collision energies is an excellent tool for identification and quantitation of different classes of lipids.

Sciex TripleTOF 5600

The TripleTOF 5600+ System combines SCIEX’s Triple Quad technology with an Accelerator TOF Analyzer, offering both nominal and accurate mass measurements on a single platform. It supports comprehensive qualitative exploration, rapid profiling, and high-resolution quantitation workflows. This system is ideal for pharmaceutical development, omics research, and analyzing unknown compounds. Its high-resolution, high-sensitivity data and fast acquisition rates make it a versatile and powerful tool for mass spectrometry.