SHUBHAM KAUSHIK
Salzburg
Quote
Every problem is a gift—without problems we would not grow.
Tony Robbins
Summary
Bioinformatician and trained mass spectrometrist with 5+ years of experience in proteomics and metabolomics. Proven problem-solver with strong analytical skills, thriving in fast-paced, collaborative research environments. Currently a researcher at PLUS Salzburg, leading projects that advance scientific discovery.
Overview
6
6
years of professional experience
2
2
years of post-secondary education
Work History
Researcher
Paris Lodron University of Salzburg
Salzburg, Austria
10.2024 - Current
- 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.
Bioinformatics Scientist (Metabolomics)
Elucidata Data Consulting
San Francisco, CA
05.2024 - 08.2024
- 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.
Scientist (LCMS) / Manager
Vproteomics (Valerian Chem Private Limited)
New Delhi
11.2022 - 05.2024
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.
LCMS Analyst
ThermoFIsher Scientific India Ltd
Gujarat
03.2022 - 11.2022
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
Application Specialist
Vproteomics (Valerian Chem Private Limited)
New Delhi
07.2019 - 03.2022
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.
Timeline
Ph.D. - Bioanalytics
Paris Lodron University of Salzburg
10.2024 - Current
Researcher
Paris Lodron University of Salzburg
10.2024 - Current
Bioinformatics Scientist (Metabolomics)
Elucidata Data Consulting
05.2024 - 08.2024
Scientist (LCMS) / Manager
Vproteomics (Valerian Chem Private Limited)
11.2022 - 05.2024
MBA - Information Technology And Project Management
Bharti Vidyapeeth Deemed University
07.2022 - 06.2024
LCMS Analyst
ThermoFIsher Scientific India Ltd
03.2022 - 11.2022
Application Specialist
Vproteomics (Valerian Chem Private Limited)
07.2019 - 03.2022
Master of Science (Bioinformatics) -
Jamia Millia Islamia
Bachelor of Science (Biochemistry) -
Monad University
Education
Ph.D. - Bioanalytics
Paris Lodron University of Salzburg
Salzburg 10.2024 - Current
MBA - Information Technology And Project Management
Bharti Vidyapeeth Deemed University
Pune 07.2022 - 06.2024
Master of Science (Bioinformatics) -
Jamia Millia Islamia
New Delhi, India06.2019
Bachelor of Science (Biochemistry) -
Monad University
06.2017
Accomplishments
- Represented ThermoFisher Scientific and GBU to Rt Hon Boris Johnson MP during India visit during July, 2022.
- Recipient of DBT BTISnet studentship fellowship during Internship at IARI, 2019
- Secured University Rank-1 during Bachelor of Science (Biochemistry) in 2017.
Languages
Hindi
First Language
English
Advanced (C1)
C1
Japanese
Elementary (A2)
A2
German
Beginner
A1
Training and Internships
- 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
- Completed 2 month training in Clinical Biochemistry lab, VMMC and Safdarjung Hospital, New Delhi.
Strength and Interpersonal skills
Technical Skills
- Technical Proficiency: Experienced in advanced laboratory techniques, including Mass Spectrometry and Chromatography, with proficiency in data analysis software.
- Programming Skills: Fluent in R and perl languages and function packages used for mass spectrometry based Omics data analysis.
- Method development: Experienced in targeted method development for clinical
- Expertise in Sample Preparation: Sample preparation for Secretomics, Interactomics, In sol (SP3, SP4 and On column digestions) and In Gel digestions for Proteomics, Phosphoenrichment on tissues (heart valve tissues, liver tissue, muscle tissues etc.), mammalian and bacterial cell lines using TiO2 magnetic beads.
- Experience on Quantitative proteomics approaches: completed major projects with Label-free quantitation, iTRAQ, TMT and few projects with Dimethyl labeling.
Professional Competencies:
- Teamwork, Leadership and Management: Demonstrated ability to manage lab operations and lead teams effectively with teamwork, overseeing wet lab work, bioinformatics, and LCMS operations.
- Problem-Solving: Skilled in developing protocols and procedures to optimize research workflows and achieve project goals.
- Communication: Strong communicator with a collaborative approach, working closely with interdisciplinary teams to support research endeavors.
- Adaptability: Adaptable to dynamic work environments, resilient in overcoming challenges, and ensuring timely project completion.
Publications
- Choudhary, M., Kaushik, S., Kapil, A., Shrivastava, R., Vashistt, J., 2022. Decoding Acinetobacter baumannii biofilm dynamics and associated protein markers: proteomic and bioinformatics approach. Archives of Microbiology 204. https://doi.org/10.1007/s00203-022-02807-y
- Singh, D., Yadav, R., Kaushik, S., Wadhwa, N., Kapoor, S., Kapoor, M., 2020. Transcriptome Analysis of ppdnmt2 and Identification of Superoxide Dismutase as a Novel Interactor of DNMT2 in the Moss Physcomitrella patens. Frontiers in Plant Science 11. https://doi.org/10.3389/fpls.2020.01185
- Virmani, S., Arora, A., Kaushik, S., Suman, A., 2023. Lignin Degradation by Isolated Lignolytic Acinetobacter baumanii S2, Aspergillus niger SF4 and Rhodotorula glutinis and Profiling Products from Bio-Valorization Perspective. Waste and Biomass Valorization 15, 101–114. https://doi.org/10.1007 /s12649-023-02140-5
- Singh, J., Kaushik, S., Maharana, C., Jhingan, G.D., Dhar, D.W., 2023. Elevated inorganic carbon and salinity enhances photosynthesis and ATP synthesis in picoalga Picocystis salinarum as revealed by label free quantitative proteomics. Frontiers in Microbiology 14. https://doi.org/10.3389/fmicb.2023.1059199
Hobbies And Interests
- Walking & Hiking
- SInging and listening to Music
- Watching Movies
- Analytical Thinking & Problem Solving
- Reading
- Learning New Tools & Techniques
- Creative Writing or Journaling
- Volunteering or Community Involvement
References
References available upon request.