Metaproteomics Foundations & Data Integration — Hands-on

Learn how to move from microbiome mass spectrometry data to taxonomically and functionally resolved protein profiles. This module covers metaproteomics experimental design, MS data processing, peptide and protein inference and strategies to integrate metaproteomics with metagenomics and metabolomics for ecological and AMR relevant insights.

Metaproteomics Foundations & Data Integration

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Session Index

Session 1 — Metaproteomics Concepts & Experimental Design Session 2 — Search Engines, PSMs & Protein Inference Session 3 — Quantitation, Annotation & Statistics Session 4 — Mini Capstone: Multi Omics Data Integration

Session 1

Fee: Rs 8800

Metaproteomics Concepts & Experimental Design

What metaproteomics measures in microbiome studies

proteins as realised function linking to metagenome and transcriptome clinical, environmental and bioprocess contexts

Sample prep and fractionation strategies for complex matrices

protein extraction from stool, soil, bioreactors surfactants and removal of inhibitors prefractionation for depth vs throughput

LC MS acquisition modes and design considerations

DDA and DIA overview instrument settings and gradients technical replicates and batch planning

Session 2

Fee: Rs 11800

Search Engines, PSMs & Protein Inference

Database construction for metaproteomics searches

using metagenome derived protein databases reference proteomes and decoy sequences database size and search speed trade offs

Peptide spectrum matches and FDR control

search engines such as MaxQuant and MSFragger target decoy strategy PSM, peptide and protein level FDR

Protein inference in mixed communities

shared peptides and protein groups resolving taxa from peptide evidence export formats for downstream analysis

Session 3

Fee: Rs 14800

Quantitation, Annotation & Statistics

Quantitation strategies for microbiome proteomes

spectral counting and LFQ intensity iBAQ and label based options normalisation across runs and batches

Taxonomic and functional annotation of proteins

mapping to KEGG, eggNOG and GO taxon to function linkage summarising pathways and subsystems

Basic statistics and visualisation for metaproteomics

differential abundance of proteins or pathways heatmaps and clustering linking to diversity and metadata

Session 4

Fee: Rs 18800

Mini Capstone: Multi Omics Data Integration

From raw MS files to annotated metaproteome table

theory plus guided practical

Integrating metaproteomics with metagenomics and metabolomics

linking proteins to MAGs and taxa overlaying metabolic pathways interpreting functional shifts and AMR signals

Deliverables: workflow outline, annotated table and report

protein and pathway summary tables analysis notebook in R or Python PDF or HTML interpretation report

PDF

Metaproteomics Foundations & Data Integration Training | Microbiome Protein Function & Multi Omics

Metaproteomics Foundations & Data Integration — Hands-on