Akhilesh Pandey, M.D., Ph.D.

Technologies

Mass Spectrometers

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.

Proteomics

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.

Liquid Chromatoraphy

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.

Highthroughput Analysis by Automation

Highthroughput analysis by automation is a part of the systems biology approach employed by our laboratory.

Metabolomics

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 hydrophobic 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.

Lipidomics

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

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. 

Bioinformatics

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

Machine learning is a part of the systems biology approach employed by our laboratory.

Peptide Synthesis and Arrays

Peptide synthesis and arrays are a part of the systems biology approach employed by our laboratory.

Multiplexed Assays (Olink)

Multiplexed assays by Olink is a part of the systems biology approach employed by our laboratory.

Thermal Proteome Profiling

Thermal proteome profiling is a part of the systems biology approach employed by our laboratory.

Glycomics

Glycomics is a part of the systems biology approach employed by our laboratory.

Capillary Electrophoresis

Capillary electrophoresis is a part of the systems biology approach employed by our laboratory.

Tissue Microarrays

Tissue microarrays are a part of the systems biology approach employed by our laboratory.