Database Search Engines, FDR and Decoy Strategies — Hands-on

Learn how tandem MS spectra are converted into confident peptide and protein level identifications. This module focuses on the concepts behind database search engines, scoring, target decoy based FDR estimation and filtering strategies so that you can benchmark and interpret search results for discovery and targeted proteomics studies.

Database Search Engines, FDR and Decoy Strategies

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Session Index

Session 1 — PSM & Database Search Concepts Session 2 — Scores, Thresholds & Target Decoy FDR Session 3 — PSM, Peptide & Protein Level Filtering Session 4 — Search Strategy Design & Reporting

Session 1

Fee: Rs 8800

PSM & Database Search Concepts

From MS/MS spectra to peptide spectrum matches (PSMs)

theoretical vs observed spectra search space definition search candidates concept

Protein sequence databases and search space control

reference proteomes contaminants and decoys overview enzyme and missed cleavage settings

Search engines at a conceptual level

scoring of candidate PSMs search parameters and tolerances multi engine searches motivation

Session 2

Fee: Rs 11800

Scores, Thresholds & Target Decoy FDR

Search scores, e values and posterior probabilities (conceptual)

ranking PSM candidates score distributions threshold thinking

Target decoy strategies for FDR estimation

decoy construction ideas estimating false discoveries global vs local FDR intuition

Setting FDR thresholds for discovery proteomics

1 percent vs 5 percent views effect on IDs and coverage choosing cutoffs for studies

Session 3

Fee: Rs 14800

PSM, Peptide & Protein Level Filtering

Multi level FDR in proteomics data flows

PSM level control peptide level aggregation protein group concepts

Filtering strategies for quantitative studies

minimum peptide counts unique vs razor peptides handling shared peptides

Quality diagnostics on search and FDR results

score vs FDR plots concept decoy behaviour checks replicate and batch level sanity

Session 4

Fee: Rs 18800

Search Strategy Design & Reporting

Designing search and FDR strategies for a study

theory plus planning worksheet

Documenting parameters for reproducible analyses

search parameter tables FDR and filtering summaries linking to raw and mzIdentML outputs

Reporting identifications in manuscripts and submissions

minimum reporting checklists export formats for repositories supporting tables and supplements

PDF

Database Search Engines, FDR and Decoy Strategies Training | Confident Proteomics Identifications

Database Search Engines, FDR and Decoy Strategies — Hands-on