Publications by authors named "Pratik D Jagtap"

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Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.
Andrew T Rajczewski, Subina Mehta, Reid Wagner, Wassim Gabriel, James Johnson, Pratik D Jagtap

J Proteomics· January 2026

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A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.
Subina Mehta, Reid Wagner, Katherine T Do, James E Johnson, Fengchao Yu, Pratik D Jagtap

bioRxiv· December 2025

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Comprehensive protease specificity profiling.
Bo Zhu, Michael D Lane, Joshua A Baller, Pratik D Jagtap, Timothy J Griffin

bioRxiv· September 2025

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The microbiologist's guide to metaproteomics.
Tim Van Den Bossche, Jean Armengaud, Dirk Benndorf, Jose Alfredo Blakeley-Ruiz, Madita Brauer, Pratik D Jagtap

Imeta· June 2025

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Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.
Andrew T Rajczewski, J Alfredo Blakeley-Ruiz, Annaliese Meyer, Simina Vintila, Matthew R McIlvin, Pratik D Jagtap

Proteomics· May 2025

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Benchmarking Spectral Library and Database Search Approaches for Metaproteomics Using a Ground-Truth Microbiome Dataset.
Andrew T Rajczewski, Subina Mehta, Reid Wagner, Wassim Gabriel, James Johnson, Pratik D Jagtap

bioRxiv· May 2025

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Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.
Andrew T Rajczewski, J Alfredo Blakeley-Ruiz, Annaliese Meyer, Simina Vintila, Matthew R McIlvin, Pratik D Jagtap

bioRxiv· January 2025

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Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.
Jesenia M Perez, Jolene M Duda, Joohyun Ryu, Mihir Shetty, Subina Mehta, Pratik D Jagtap

Sci Rep· January 2025

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Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.
Diana Samodova, Evelina Stankevic, Mathilde Sonne Søndergaard, Naiyu Hu, Tarunveer S Ahluwalia, Pratik D Jagtap

Microbiome· January 2025

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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease.
Katherine Do, Subina Mehta, Reid Wagner, Timothy J Griffin, Pratik D Jagtap

J Vis Exp· January 2025

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Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.
Praveen Kumar, James E Johnson, Thomas McGowan, Matthew C Chambers, Mohammad Heydarian, Pratik D Jagtap

Methods Mol Biol· October 2024

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Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.
Sarah Samorodnitsky, Monica Kruk, Eric F Lock, Ken M Kunisaki, Alison Morris, Pratik D Jagtap

Respir Res· September 2024

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An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.
Monica E Kruk, Subina Mehta, Kevin Murray, LeeAnn Higgins, Katherine Do, Pratik D Jagtap

mSystems· July 2024

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A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.
Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T Rajczewski, Pratik D Jagtap

mSphere· June 2024

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Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.
Sarah Samorodnitsky, Monica Kruk, Eric F Lock, Ken M Kunisaki, Alison Morris, Pratik D Jagtap

Res Sq· June 2024

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A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.
Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T Rajczewski, Pratik D Jagtap

bioRxiv· December 2023

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A Galaxy of informatics resources for MS-based proteomics.
Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Föll, Pratik D Jagtap

Expert Rev Proteomics· November 2023

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The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).
Pratik D Jagtap, Michael R Hoopmann, Benjamin A Neely, Antony Harvey, Lukas Käll

J Biomol Tech· September 2023

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Metaproteomic Analysis of Nasopharyngeal Swab Samples to Identify Microbial Peptides in COVID-19 Patients.
Surbhi Bihani, Aryan Gupta, Subina Mehta, Andrew T Rajczewski, James Johnson, Pratik D Jagtap

J Proteome Res· August 2023

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Integrative meta-omics in Galaxy and beyond.
Valerie C Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Pratik D Jagtap

Environ Microbiome· July 2023

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2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.
Joanna Kirkpatrick, Paul M Stemmer, Brian C Searle, Laura E Herring, LeRoy Martin, Pratik D Jagtap

J Biomol Tech· July 2023

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An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples.
Danielle O Weise, Monica E Kruk, LeeAnn Higgins, Todd W Markowski, Pratik D Jagtap

Clin Proteomics· April 2023

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Galaxy Training: A powerful framework for teaching!
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Pratik D Jagtap

PLoS Comput Biol· January 2023

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Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations.
Subina Mehta, Valdemir M Carvalho, Andrew T Rajczewski, Olivier Pible, Björn A Grüning, Pratik D Jagtap

Viruses· October 2022

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An overview of technologies for MS-based proteomics-centric multi-omics.
Andrew T Rajczewski, Pratik D Jagtap, Timothy J Griffin

Expert Rev Proteomics· March 2022

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