Pratik Jagtap

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Comparative Evaluation of DDA- and DIA-Based Proteomic Workflows in Beryllium-Related Lung Disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-06-09

• Molecular characterisation of progressive pulmonary sarcoidosis: protocol for a longitudinal multi-centre study to develop peripheral blood circulating biomarkers for predicting pulmonary sarcoidosis progression

  BMJ Open · 2026-04-01

• Comprehensive proteomic classifier for molecular characterisation of pulmonary sarcoidosis: protocol for a longitudinal multi-centre study to evaluate bronchoalveolar fluid and cell diagnostic and prognostic biomarkers of pulmonary sarcoidosis

  BMJ Open · 2026-04-01

• iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

  Genome biology · 2026-02-25

• The need for standardisation and improved open (meta)data practices in metaproteomics

  ChemRxiv · 2025-12-04 · 1 citations

• Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset

  Journal of Proteomics · 2025-10-22

• Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiomePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-15

• Comparative Performance of Scribe and Database Search Engines in Metaproteomic Profiling of a Ground-Truth Microbiome DatasetPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-20

• The microbiologist's guide to metaproteomics

  iMeta · 2025-05-06 · 48 citations

• Data‐Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

  PROTEOMICS · 2025-04-10 · 15 citations

• A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidatesPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-08

• The Microbiologist’s Guide to MetaproteomicsPreprint

  ChemRxiv · 2025-04-01 · 1 citations

• A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

  Journal of Visualized Experiments · 2025-01-10

• The Microbiologist’s Guide to MetaproteomicsPreprint

  ChemRxiv · 2025-01-08 · 4 citations

• Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer

  Scientific Reports · 2025-01-04 · 3 citations

• Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial dataPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-12-27 · 2 citations

• Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

  Biogeosciences · 2024-11-08 · 12 citations

• Comprehensive protease specificity profilingPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-07 · 2 citations

• Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform

  Methods in molecular biology · 2024-10-22 · 3 citations

• The lung proteome in HIV-associated obstructive lung disease

  ERJ Open Research · 2024-09-27 · 2 citations