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Integrative Proteomics & Peptidomics (Proteogenomics) Training | IDs, Quant, PTMs & Multi-omics

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Proteomics, Structural Bioinformatics, Molecular Modeling >> Integrative Proteomics & Peptidomics (Proteogenomics) Training | IDs, Quant, PTMs & Multi-omics

Integrative Proteomics & Peptidomics (Proteogenomics) — Hands-on

Build end-to-end proteomics and peptidomics pipelines, then integrate them with transcriptomics and genomes for proteogenomic discovery. Learn search/ID, quantification (LFQ/TMT/DIA) , PTM mapping, variant/novel peptide detection, and biological interpretation with robust QC and reporting.

Integrative Proteomics & Peptidomics (Proteogenomics)
Help Desk · WhatsApp
Session 1
Fee: Rs 6300
MS IDs, Databases & FDR
  • Spectra → peptide IDs: search engines & parameters; target–decoy & FDR
    • Theory
  • Tools & workflows (overview)
    • MaxQuant Proteome Discoverer MSFragger/Comet/Mascot* Percolator/PeptideProphet
  • Protein inference, PTM site localization & QC
    • Ascore/PTMProphet multi-enzymes/open search
Session 2
Fee: Rs 8400
Quantification: LFQ/TMT/DIA
  • Label-free vs isobaric vs DIA: design, batch effects & normalization
    • LFQ (MaxLFQ) TMT/iTRAQ DIA-NN/Spectronaut*
  • Missing values, imputation & differential abundance
    • MSstats/Limma combat/batch removal
  • PTM-centric quant & site occupancy (phospho etc.)
    • localization probabilities motif enrichment
Session 3
Fee: Rs 11200
Peptidomics & Proteogenomics
  • Endogenous peptide-centric analyses (processing & QC)
    • semi-/no-enzyme searches de novo (PEAKS*/Novor)
  • Proteogenomics: custom FASTAs & variant/neoantigen peptides
    • RNA-seq-guided FASTA novel junctions/SNVs open modification search
  • Pathways & interaction maps from proteomic signatures
    • GSEA/ssGSEA/ORA STRING/Cytoscape
Session 4
Fee: Rs 14000
Mini Capstone: Cohort Proteogenomics
  • Process a small cohort: ID → quant → PTM/variant peptides → pathways
    • Theory + Practical
  • Build a reproducible report bundle with provenance & QC gates
    • Snakemake/Nextflow Quarto/Markdown manifest/checksums
  • Deliverables: figures, tables, README & manifest
    • PDF CSV/TSV HTML


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