SHUBHAM KAUSHIK

• Working on capillary columns to adapt for low sample amounts from EVs, phosphoenrichments.
• Method developments and improvements for mass spectrometry-based omics data acquisition.
• Sample preparation, MS method development, data acquisition, and data analysis followed by bioinformatics analysis.

• Worked on Mass spectrometry imaging based metabolomics data analysis using different packages incl. Cardinal, Isoscope, etc.
• Involved in pathway visualization application testing and development for metabolomics datasets.
• Participated in weekly team meetings to discuss progress towards project goals and collaborate on solutions.
• Prepared reports summarizing research results for presentation to colleagues and management.

Project Contributions and Development:

• Contributed significantly to the standardization of phosphoenrichment protocols for both mammalian and bacterial samples, identification of various Post-Translational Modifications (PTMomics), Interactomics, Secretomics using high-resolution mass spectrometry.
• Engaged in method development for the absolute quantification of immunosuppressants in plasma samples, newborn screening in dried blood spots (DBS) for amino acids and carnitines, analysis of aromatic amino acids in plant extracts, and quantification of curcumin in plasma using LCMS.

Laboratory Management and Leadership:

• Led and managed various research projects from conception to completion, ensuring quality results and timely delivery.
• Manage and oversee all operations of the LC-MS facility, including wet lab work, bioinformatics, and LCMS operations.
• Train and mentor staff and students on LCMS operations, wet lab techniques, and bioinformatics analysis.
• Coordinate and collaborate with researchers from diverse scientific disciplines to support their projects and research goals.

Laboratory Skills and Methodologies:

• Skilled in various extraction techniques for lipids, metabolites, and proteins from plant tissues, animal tissues, and cell lines.
• Experienced in a wide range of digestion techniques, including in-solution digestion, on-column digestion, SP3, SP4, and in-gel digestion methods (silver and Coomassie stained), as well as from 2D-spots.
• Expertise in enrichment methods such as phosphoenrichment of mammalian tissues, cell lines, and bacterial lysates.

Instrumentation Proficiency:

• Proficient in operating a diverse range of Mass Spectrometers, including Orbitrap Exploris 240, QExactive, QExactive Plus, Quantis, Altis, and Quantum Ultra.
• Skilled in utilizing different Chromatographic Systems such as the Dionex Ultimate 3000, Nanolc1000, Nanolc1200, Easynlc 1000, Easynlc 1200, RSLCnano, and Vanquish.
• Experienced in routine cleaning, calibration, troubleshooting, and maintenance of Mass Spectrometers and related equipment.

Data Analysis and Software Skills:

• Proficient in data analysis using software tools like Proteome Discoverer 3.0, Compound Discoverer 3.2, and LC Quan, Lipid Search for lipid data analysis.
• Developed in-house data analysis pipelines using R and script processing pipelines using Perl.

Instrumentation: Orbitrap Exploris 240

Software's: Proteome Discoverer, Compound Discoverer

Perform routine Calibration, Tuning and mass spectrometry based protoemics and metabolomics experiments

Cleaning and Trouobleshooting for instrumentation

Instrumentation: QExactive

Software's: Proteome Discoverer and statistical analysis using R scripts

Perform routine Calibration, Tuning and proteomics method developments.

Worked at CIF, University of Delhi South Campus and CDC, Banaras Hindu University.

Doctoral studies on method developments and multiomics characterization on Extracellular vesicles using advanced mass spectrometry, University of Salzburg, Supervisor: Prof. Christian Huber

Summary: Worked on project entitled "PPlncRNAdb: Putative peptides translated from non-coding RNAs in plants" at Bioinformatics facility under supervision of Dr. Amrendra Sharma at ICAR-IARI, New Delhi.

CGPA: 8.98

Major Subjects:

Biochemistry, Microbiology, Genetics, Molecular Biology, Immunology, Clinical Biochemistry, Bioenergetics and Metabolism, Plant Biochemistry, Cell Biology.

Percentage: 82.05 %