State-of-the-art mass spectrometry is at the core of our research and technology development right from identification of proteins, post-translational modifications, lipids and metabolites in various cancers and disease settings to its deployment in advanced diagnostics and clinical assay development. Over the last few years, mass spectrometry as an analytical instrument for characterizing proteins, lipids and small molecules has become an important tool to transform research from bench to bedside. Our lab is engaged in developing mass spectrometry-based clinical assays that can be used routinely for diagnostics, disease monitoring and patient therapy.
Pandey lab has pioneered the use of in vivo labeling using SILAC and in vitro tandem mass tags (TMT) peptide labeling. Recently, we developed BioSITe for studying proximity-based protein-protein interactions. We characterize various post-translational modifications such as phosphorylation, acetylation, biotinylation, ubiquitination, glycosylation in our quest to identify potential therapeutic targets in cancer. We are engaged in developing novel enrichment methods for the O-linked glycosylated peptides. We are also using data-independent acquisition (DIA) methods for large scale profiling and validation of protein biomarkers.
Highthroughput Analysis by Automation
Highthroughput analysis by automation is a part of the systems biology approach employed by our laboratory.
Our lab has optimized advanced analysis pipelines in a targeted and untargeted metabolomics method using LC coupled to ID-X MS. Multiple reaction monitoring (MRM) method, classic targeted quantification, has been used to find biomarker metabolites in many diseases. Our lab has used reverse phase liquid chromatography (RPLC) for non-polar molecules and hydrophilic interaction liquid chromatography (HILIC) for polar molecules not retained by RPLC. Using untargeted metabolomics approach, we are able to identify and semi-quantify about 1,000 metabolites at once.
We use RPLC coupled with state-of-the-art high resolution MS for untargeted and targeted lipidomics of various classes of lipids such as phospholipids, sphingolipids, glycerols and sterols. We identify hundreds of individual lipid molecular species based on precursor ion mass and tandem MS spectra from biological samples such as serum, plasma, cerebrospinal fluid and cell pellets using cutting-edge ID-X MS from Thermo Fisher Scientific. Data-dependent mode with AcquireX data acquisition can expand the coverage of lipids identified by automatically generating the exclusion and inclusion list upon injection of blank and sample of interest.
Next-generation Sequencing (NGS) has been successfully employed in molecular characterization of many diseases and cancers. On the other hand, RNA-seq, Ribo-seq, Hi-C and bisulfate helped in molecular profiling of tissue and cell types. Recent innovations in single cell sequencing and portable platforms like Nanopore push the limits to sequence DNA from any sample bringing translational medicine to field and bed side.
Emergence of high-throughput technologies has made possible systematic identification and quantification of vital biological molecules including DNA, RNA, proteins and various metabolites. Development of computational methods to process, compare and interpret the raw data from such technologies is also vital for faster and accurate analysis to make useful biological interpretations. Understanding the mechanism of a disease by studying one level of –omics data is insufficient to design precise diagnostic, treatment and prognostic approaches. Computational methods for integrative analysis of cross platform datasets requires good understanding of individual technologies and their limitations.
Machine learning is a part of the systems biology approach employed by our laboratory.
Peptide synthesis and arrays are a part of the systems biology approach employed by our laboratory.
Thermal Proteome Profiling
Thermal proteome profiling utilizes the phenomenon that proteins are thermally stabilized by the presence of ligands and lead to a higher melting temperature. We deploy TMT-based multiplexing proteomics to identify the effectors of drug treatment. It allows unbiased search of drug targets and can be applied in living cells thereby facilitating identification of markers of drug efficacy and toxicity.
Glycomics is a part of the systems biology approach employed by our laboratory.
Capillary electrophoresis is a part of the systems biology approach employed by our laboratory.
Tissue microarrays are a part of the systems biology approach employed by our laboratory.