Metaproteomics & Proteogenomics in Microbial Communities — Hands-on

Learn a complete metaproteomics and proteogenomics workflow for microbial communities. Build protein databases from metagenomes/MAGs, identify peptides with mainstream engines, control FDR, quantify proteins (LFQ/iBAQ/TMT) , and map results to taxa, pathways, and AMR/virulence functions. Includes DIA/SWATH overview, QC dashboards, and a reproducible mini-report.

Metaproteomics & Proteogenomics in Microbial Communities

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Session Index

Session 1 — Design, Sample Prep & DB Strategy Session 2 — Peptide ID, FDR & Protein Inference Session 3 — Quant (LFQ/TMT/DIA) & QA/QC Session 4 — Taxa/Function Mapping & Reporting

Session 1

Fee: Rs 8800

Design, Sample Prep & Database Strategy

Study design & LC–MS/MS overview

DDA vs DIA/SWATH fractionation & replicates spike-ins & iRT

Sample prep best practices

lysis/cleanup & digestion contamination controls batch planning

Proteogenomic DB construction

MAG/de novo gene catalogs UniProt/RefSeq+decoys redundancy & target–decoy

Session 2

Fee: Rs 11800

Peptide Identification, FDR & Protein Inference

Search engines & parameters

MS-GF+ / MaxQuant / Comet variable mods & PTMs open searches (overview)

FDR control & validation

target–decoy, Percolator PSM/protein-level q-values entrapment tests

Protein inference & grouping

razor/unique peptides shared peptide handling protein groups reports

Session 3

Fee: Rs 14800

Quantification (LFQ/TMT/DIA) & QA/QC

Quant pipelines

LFQ/iBAQ (MaxQuant) TMT/iTRAQ normalization DIA-NN/Spectronaut (overview)

QC metrics & imputation

ID rates, CVs, missingness MSstats/Perseus workflows batch effect handling

Differential protein analysis

linear models & contrasts multiple testing (FDR) volcano & heatmaps

Session 4

Fee: Rs 18800

Taxonomic/Functional Mapping & Reproducible Reporting

Taxonomic assignment (LCA)

peptide→protein→taxon link to MAGs/reads strain-level caveats

Function & pathway mapping

KO/EC/eggNOG/GO MetaCyc/KEGG pathways AMR/VF overlays

Reporting & exports

Quarto notebooks tables/figures + env files SOPs & templates

PDF

Metaproteomics & Proteogenomics in Microbial Communities Training | MaxQuant/MS-GF+, LFQ/TMT/DIA, Taxa & Pathways

Metaproteomics & Proteogenomics in Microbial Communities — Hands-on