Shotgun Proteomics — Peptide Identification & FDR — Hands-on

Learn the complete peptide and protein identification workflow used in modern shotgun proteomics. You will configure search spaces, run and tune peptide spectrum matching, understand scoring and target decoy based validation, control FDR at PSM, peptide and protein levels, and generate reviewer ready identification reports.

Shotgun Proteomics — Peptide Identification & FDR

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Session Index

Session 1 — Spectra, Search Space & Search Setup Session 2 — Peptide Spectrum Matching & Scoring Session 3 — Target Decoy, FDR & Validation Session 4 — Protein Inference, Reports & Reproducibility

Session 1

Fee: Rs 12320

Spectra, Search Space & Search Setup

Understanding tandem MS spectra for IDs

fragment series (b y) charge states & isotopes noise and intensity patterns

Database and search space definition

UniProt Swiss Prot vs TrEMBL contaminant databases enzyme rules & missed cleavages

Search parameter setup and export

precursor and fragment tolerances fixed and variable modifications open vs narrow searches overview

Session 2

Fee: Rs 16520

Peptide Spectrum Matching & Scoring

Search engines and score types

Comet MS GF plus X Tandem SEQUEST like scores XCorr, E values, hyperscore ideas

Spectrum pre processing and matching

peak picking and filtering matching theoretical vs experimental ions handling chimeric spectra

Score distributions and diagnostics

decoy vs target score curves delta score concepts search quality checks

Session 3

Fee: Rs 20720

Target Decoy, FDR & Validation

Target decoy strategies and pitfalls

reversed vs shuffled decoys concatenated vs separate decoy inflation issues

Multi level FDR estimation

PSM FDR and q values peptide and protein FDR percolator like rescoring ideas

Confidence thresholds and validation workflows

one percent FDR conventions site level vs peptide level control manual spectrum review guidelines

Session 4

Fee: Rs 26320

Protein Inference, Reports & Reproducibility

Protein inference and parsimony rules

shared peptides handling razor peptides concept protein grouping and sub grouping

Export tables, evidence tracking and checklists

PSM, peptide and protein tables sequence coverage plots minimal information for proteomics reports

Reproducibility and repository submission overview

search parameter documentation pipeline versioning PRIDE submission concepts

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Shotgun Proteomics — Peptide Identification & FDR Training | Search Space, Scoring, Target–Decoy & Multi level FDR

Shotgun Proteomics — Peptide Identification & FDR — Hands-on