Proteomics Facility at IOB


Institute of Bioinformatics (IOB) has been a pioneer of Omics technologies and research in India since 2002. Established in 2008 by Dr. Akhilesh Pandey, the Proteomics Facility at IOB has been providing expertise, services, education and training to enhance biomedical research through mass spectrometry-based proteomics. Our goal is to enable investigators employ proteomics in their biomedical research on projects ranging from differential proteomics to understanding disease mechanisms to identifying therapeutic targets or protein interactors. In its endeavor to assist the scientific community in India, the Proteomics Facility at IOB has provided its expertise to researchers from a number of leading academic institutes including ACTREC (Mumbai), NIRRH (Mumbai), NIMR (Goa), NII (New Delhi), and Cancer Institute (WIA, Chennai) among others. The personnel in the Proteomics Facility at IOB include a dedicated team of skilled mass spectrometrists, proteomics experts and computational biologists who can provide help from design of an optimal experiment to choosing the most appropriate strategy and taking the users all the way to the publication stage.

The Proteomics Facility at IOB houses state-of-the-art proteomics equipment including high resolution Fourier Transform Orbitrap mass spectrometers and high performance liquid chromatography systems. Access to modern instrumentation combined with decades of experience in proteomics and mass spectrometry allows the users to obtain comprehensive and sensitive proteomics analysis that is not routinely available at most core facilities not just in India but in the world. As an integral part of a leading systems biology research institute, the Proteomics Facility at IOB is committed to providing the latest and best in proteomics technologies at reasonable costs to the scientific community.


The Proteomics Facility at IOB is equipped to provide services related to qualitative and quantitative analyses of proteomes (e.g. TMT, SILAC and label-free based quantitation). The facility also assists with computational analysis and in the development of customized applications for isolation, detection, characterization and quantitative analysis of post-translational modifications such as phosphorylation, acetylation and ubiquitylation. We aim to expand our services to include targeted proteomics in the near future.


We provide following proteomics services to external researchers including industry:


Qualitative proteomics

Protein identification

Global proteome profiling

Interactome proteomics (IP-MS)

Quantitative proteomics

Label-free quantitaion

Label-based quantitation

Post-translational modifications





For pricing related to your study, please send an e-mail to proteomics at ibioinformatics dot org along with details of your experiment


The Proteomics Facility is equipped with the state-of-the-art Fourier Transform Orbitrap mass spectrometers and liquid chromatography platforms to provide comprehensive, accurate and sensitive proteomics services to researchers.


Mass spectrometers

QExactive Plus mass spectrometer

QExactive Plus mass spectrometer

QExactive Plus is a hybrid Quadrupole-Orbitrap mass spectrometer that introduces a revolutionary concept of Quanfirmation. It has an ability to confirm and quantify, identify, in a single analysis. QExactive with its maximized performance and reliability is ideal for both large- and small-molecule applications. With Advanced quadrupole technology (AQT) this instrument is equipped to perform sophisticated data-independent analysis (DIA) and parallel reaction monitoring (PRM) providing reproducible quantitation results while delivering complete qualitative confidence. An optional Protein Mode enhances analysis of intact proteins through sophisticated ion beam control and easy pressure adjustment, while optional 280,000 maximum resolution ensures maximum ID confidence in top down and Lipidomics as well as in small molecule applications.


Orbitrap Velos mass spectrometer

Orbitrap Velos mass spectrometer

LTQ Orbitrap Velos mass spectrometer is a hybrid Fourier Transform mass spectrometer boasting an ultra-high resolving power >100,000 with low attomole level sensitivity. This high-performance LC-MS and MSn system is equipped with a dual-pressure linear ion trap for rapid data acquisition coupled to the high mass accuracy Orbitrap mass analyzer. LTQ Orbitrap Velos has higher-energy C-trap dissociation (HCD) and electron transfer dissociation (ETD) fragmentation regimes in addition to LTQ’s collision-induced dissociation (CID) option. These alternative fragmentation capabilities are particularly useful for analyzing post-translational modifications like phosphorylation and glycosylation. LTQ-Orbitrap Velos is routinely used for both qualitative and quantitative proteomics studies including characterization of post-translational modifications.


Liquid Chromatography System

Thermo Scientific Easy n-LC 1000

Thermo Scientific Easy n-LC 1000

The Thermo Scientific EASY-nLC 1000 system interfaced with the LTQ Orbitrap Velos-ETD mass spectrometer provides effortless peak performance for nanoflow applications up to 1000 bar. Dual in-line flow sensors before solvent mixing give excellent gradient precision. Its intuitive software facilitates rapid method setup and immediate system control.


Agilent 1200-infinity series HPLC systems

Agilent 1200-infinity series HPLC systems

The proteomics facility houses two 1200 series HPLC systems from Agilent Technologies as a standalone offline fractionation system. In most projects, we carry out offline fractionation of proteins/peptides using various LC based techniques such as strong cation exchange chromatography (SCX), anion exchange chromatography (SAX) and macroporous reversed phase chromatography. We also employ multiple affinity removal systems for depletion of abundant proteins from serum, cerebrospinal fluid or other body fluids.


Fractionation System

Gel-free Fractionation System

Gel-free Fractionation System

We have one Gelfree 8100 Protein Fractionation System from expedeon. The GELFREE 8100 Fractionation System provides a quick, simple and reproducible method for partitioning complex protein samples into discrete molecular weight-based fractions. This novel method of fractionation eliminates the need for band or spot cutting, making it possible to isolate proteins over a broad mass range in 90 minutes.


Agilent 3100 OFFGEL Fractionator

Agilent 3100 OFFGEL Fractionator

The proteomics facility houses an Agilent 3100 OFFGEL Fractionator. This is an offline fractionation technique for protein and peptides based on isoelectric focusing technology. We are using this instrument for our proteomic investigations.


Other instruments


Multiskan GO UV/Vis Spectrophotometer


Vacuum Concentrator


For pricing details for your particular case study, please write to proteomics at ibioinformatics dot org. Prices may vary depending upon the sample complexity, fractionation and enrichment, gradient length, sample size and number of replicates. It is advisable to discuss the proposed objective, experimental design and sample details with us before submitting the samples.

Basic data analysis will be provided. For detailed analysis and advanced searches, users can ask for the cost estimate.

In case you are writing a paper with data generated from our facility, you can simply acknowledge the facility.

We are currently accepting samples for global and quantitative analysis of proteomes and phosphoproteomes.


Proteomics Facility
Institute of Bioinformatics
7th Floor
Discoverer Building
International Tech Park Limited
Bangalore, Karnataka-560066
Phone: +91-80-2841-6140
Fax: +91-80-2841-6132
Email: proteomics at ibioinformatics dot org