False Discovery Control & Levels of Identification (MSI) — Hands-on

Make your metabolomics results statistically and chemically trustworthy. This module connects multiple testing and FDR control with LC–MS/GC–MS feature curation, decoy and blank strategies, and Metabolomics Standards Initiative (MSI) identification levels so that you can report features and metabolite IDs with clear, defendable confidence.

False Discovery Control & Levels of Identification (MSI)

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Session Index

Session 1 — Multiple Testing, FDR & q-Values in Metabolomics Session 2 — Decoys, Blanks & QC Based False Positive Control Session 3 — Identification Confidence & MSI Levels in Practice Session 4 — Mini Capstone: FDR & ID Confidence Report

Session 1

Fee: Rs 8800

Multiple Testing, FDR & q-Values in Metabolomics

Why multiple testing explodes in untargeted feature tables

thousands of features p-value inflation false discovery concepts

From p-values to FDR and q-values

Benjamini Hochberg overview q-value interpretation setting FDR thresholds

Feature level significance reporting for metabolomics tables

adjusted p-values volcano plots (concepts) effect sizes and fold changes

Session 2

Fee: Rs 11800

Decoys, Blanks & QC Based False Positive Control

Using blanks and QCs to identify artifactual features

blank dominated signals carryover and contamination QC coefficient of variation

Decoy based strategies to estimate false discovery rates

target decoy logic (concepts) shuffling or randomization ideas empirical FDR curves

Combining statistical and experimental evidence for filtering

blank filters plus FDR presence and intensity rules transparent decision criteria

Session 3

Fee: Rs 14800

Identification Confidence & MSI Levels in Practice

Recap of MSI levels and what they mean in real datasets

Level 1 through Level 4 when to upgrade or downgrade IDs common pitfalls and overclaims

Evidence matrices for each candidate identification

accurate mass and RT support MS/MS pattern quality adduct and isotope consistency

Feature level vs ID level uncertainty and FDR thinking

significant feature sets candidate metabolite lists communicating uncertainty

Session 4

Fee: Rs 18800

Mini Capstone: FDR & ID Confidence Report

Apply FDR control and filtering to a small metabolomics dataset

Theory + Practical

Attach MSI levels and evidence columns to selected IDs

MSI level annotation evidence and notes fields flags for low confidence hits

Deliverables: feature list with q-values and ID confidence

q-value annotated feature table (CSV) MSI level and evidence table short FDR and ID confidence summary

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False Discovery Control & Levels of Identification (MSI) Training | FDR, q-Values & Confidence

False Discovery Control & Levels of Identification (MSI) — Hands-on