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Clinical Proteogenomics & Biomarker Panels | DDA/DIA, PTMs & Targeted Assays

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> Clinical & Translational Bioinformatics / Precision Medicine >> Clinical Proteogenomics & Biomarker Panels | DDA/DIA, PTMs & Targeted Assays

Clinical Proteogenomics & Biomarker Panels — Hands-on

Design and operate clinical-grade proteogenomics workflows that connect variants and expression to protein evidence. This module covers MS-based discovery (DDA/DIA) , peptide-spectrum matching, protein inference, PTM/phosphoproteomics, targeted assay development (PRM/SRM/MRM) , quality metrics, and multi-omics integration for validated biomarker panels and reports.

Clinical Proteogenomics & Biomarker Panels
Help Desk · WhatsApp
Session 1
Fee: Rs 18920
Proteomics Foundations & QC
  • Acquisition & data formats
    • DDA vs DIA basics mzML/mzIdentML FASTA/decoys
  • Quality metrics & controls
    • mass accuracy/RT drift carryover/blank checks iRT/standards
  • Pipelines & toolchain
    • MaxQuant/MSFragger FragPipe/Proteome Discoverer DIA-NN/OpenSWATH
Session 2
Fee: Rs 23120
Discovery (DDA/DIA) & Protein Inference
  • PepID & FDR control
    • target–decoy Percolator/PSM q-values site-level FDR
  • Spectral libraries & DIA
    • library-free vs library-based transition selection interference handling
  • Protein inference & quant
    • razor/unique peptides LFQ/iBAQ missingness & imputation
Session 3
Fee: Rs 27320
PTMs/Phospho & Targeted Panels (PRM/SRM)
  • PTM identification (overview)
    • phospho enrichment open searches localization scores
  • Targeted assay design
    • peptide uniqueness stable isotope standards transition optimization
  • Panel performance & QC
    • linearity/precision LoD/LoQ matrix effects
Session 4
Fee: Rs 32920
Proteogenomics, Validation & Reporting
  • Proteogenomic mapping
    • custom variant FASTA RNA/Protein concordance neoantigen peptides (high-level)
  • Validation & governance
    • reference materials/QC charts change control & SOPs proficiency testing
  • Clinical reporting & integration
    • evidence tables FHIR/HL7 (overview) limitations & disclaimers


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