Personal profile
Research interests
Pratik Jagtap is a Research Assistant Professor at the Department of Biochemistry, Molecular Biology, and Biophysics at the University of Minnesota. He has helped manage the Galaxy-P project from its inception. His current research interests include developing analytical workflows for the analysis of complex data, with particular emphasis on MS-based proteomics applications in metaproteomics, proteogenomics, and data-independent acquisition (DIA) data analysis.
External Positions
Chair, Proteomics Research Group at the Association of Biomolecular Research Facilities
Aug 1 2018 → Jul 31 2020
Research Interest Keywords
- Metaproteomics
- Proteomics
- Bioinformatics
- Proteogenomics
- Multi-Omics
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 3 Good Health and Well-being -
SDG 4 Quality Education -
SDG 9 Industry, Innovation, and Infrastructure -
SDG 13 Climate Action -
SDG 14 Life Below Water
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Collaborations and top research areas from the last five years
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A Galaxy-based multi-omic informatics hub for cancer res
Griffin, T. J. (PI), Baller, J. A. (CoI), Hegeman, A. D. (CoI), Jagtap, P. D. (CoI), Johnson, J. E. (Other Role), Lynch, B. J. (Other Role) & Wennblom, T. (Other Role)
5/18/16 → 4/30/21
Project: Research project
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Bioinformatics Analysis of Functions Expressed by Microbiomes
Jagtap, P. D. (PI)
AMERICAN SOCIETY FOR MICROBIOLOGY
3/1/20 → 12/1/21
Project: Research project
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Pulmonary Immune Regulation of Lung Injury after Pediatric Hematopoietic Cell Transplant
Griffin, T. J. (PI), Wagner, R. (PI), Wendt, C. H. (CoI), Jagtap, P. D. (Other Role), Mehta, S. P. (Other Role) & Weise, D. O. (Other Role)
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, NIH NATL HEART, LUNG AND BLOOD INSTITU
8/20/25 → 5/31/28
Project: Research project
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An enabling approach for deep metaproteomic characterization of microbial contributors to tumorigenesis in clinical samples
Griffin, T. J. (PI) & Jagtap, P. D. (Co-Principal Investigator)
4/1/25 → 3/31/28
Project: Research project
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Comprehensive Proteomic Classifier for the Molecular Characterization of Pulmonary Sarcoidosis (MoChaS)
Drake, J. M. (PI), Griffin, T. J. (PI), Lock, E. (PI), Perlman, D. M. (PI), Hoff, I. N. (Other Role), Jagtap, P. D. (Other Role), Mehta, S. P. (Other Role) & Viken, K. J. (Other Role)
THE OHIO STATE UNIVERSITY, NIH NATL HEART, LUNG AND BLOOD INSTITU
12/2/24 → 8/31/26
Project: Research project
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Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms
Thuy-Boun, P. S., Mehta, S., Gruening, B., McGowan, T., Nguyen, A., Rajczewski, A. T., Johnson, J. E., Griffin, T. J., Wolan, D. W. & Jagtap, P. D., Feb 5 2021, In: Journal of Proteome Research. 20, 2, p. 1451-1454 4 p.Research output: Contribution to journal › Article › peer-review
Open Access20 Link opens in a new tab Scopus citations -
Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the galaxy platform
Mehta, S., Easterly, C. W., Sajulga, R., Millikin, R. J., Argentini, A., Eguinoa, I., Martens, L., Shortreed, M. R., Smith, L. M., McGowan, T., Kumar, P., Johnson, J. E., Griffin, T. J. & Jagtap, P. D., Jul 8 2020, In: Proteomes. 8, 3, 15.Research output: Contribution to journal › Article › peer-review
Open Access13 Link opens in a new tab Scopus citations -
A review of the scientific rigor, reproducibility, and transparency studies conducted by the ABRF research groups
Mische, S. M., Fisher, N. C., Meyn, S. M., Church, K. S., Hegstad-Davies, R. L., Weis-Garcia, F., Adams, M., Ashton, J. M., Delventhal, K. M., Dragon, J. A., Holmes, L., Jagtap, P., Kubow, K. E., Mason, C. E., Palmblad, M., Searle, B. C., Turck, C. W. & Knudtson, K. L., Apr 2020, In: Journal of Biomolecular Techniques. 31, 1, p. 11-26 16 p.Research output: Contribution to journal › Review article › peer-review
Open Access24 Link opens in a new tab Scopus citations -
Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset
Rajczewski, A. T., Mehta, S., Wagner, R., Gabriel, W., Johnson, J., Do, K., Vintila, S., Wilhelm, M., Kleiner, M., Searle, B. C., Griffin, T. J. & Jagtap, P. D., Jan 6 2026, In: Journal of Proteomics. 322, 105549.Research output: Contribution to journal › Article › peer-review
Open Access -
iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates
Mehta, S., Wagner, R., Do, K. T., Johnson, J. E., Yu, F., Jubenville, T., Richards, K., Coleman, S., Popescu, F. E., Nesvizhskii, A. I., Largaespada, D. A., Jagtap, P. D. & Griffin, T. J., Dec 2026, In: Genome biology. 27, 1, 111.Research output: Contribution to journal › Article › peer-review
Open Access
Datasets
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iPRG-2020: Proteome Informatics Research Group Study on Metaproteomics
Jagtap, P., Weintraub, S. T., Davis, D., Harvey, A., Hoopmann, M., Käll, L., Payne, S. H., Perez-Riverol, Y. & Palmblad, M., ZENODO, 2021
DOI: 10.5281/zenodo.4599626, https://zenodo.org/record/4599626
Dataset
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github.com/iwc-workflows/clinicalmp-verification/main
Jagtap, P., ZENODO, Mar 24 2025
DOI: 10.5281/zenodo.15078844, https://zenodo.org/records/15078844
Dataset
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The 2020 ABRF Beer Study: beer proteomics at the global scale
Phinney, B. S., Tsai, H., Marcus, A., Fox, G., Ding, H., Herring, L. E., Jagtap, P. D., Kirkpatrick, J., Kumar, V., Midha, M. K., Martin, L., Palmblad, M., Shan, B., Stemmer, P. M., Wang, Y., Polasky, D. A., Carr, A., Shortreed, M. & Neely, B. A., ZENODO, 2021
DOI: 10.5281/zenodo.5646304, https://zenodo.org/record/5646304
Dataset
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Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Rajczewski, A. & Jagtap, P., ZENODO, Aug 26 2024
DOI: 10.5281/zenodo.13376414, https://zenodo.org/records/13376414
Dataset
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Trimmed RNASeq pair for the Galaxy Training Network tutorial - "Metatranscriptomics analysis using microbiome RNASeq data"
Jagtap, P., Mehta, S. P. & Kumar, P., ZENODO, 2019
DOI: 10.5281/zenodo.3269404, https://zenodo.org/record/3269404
Dataset