Protein Identification — Database Search and FDR — Hands-on

Master the core steps of identifying proteins from LC–MS/MS data. This module walks through spectrum processing, database and FASTA preparation, search engine logic, target–decoy based FDR estimation, and validation workflows that yield high confidence peptide and protein identifications for downstream quantitative and functional analysis.

Protein Identification — Database Search and FDR

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Session Index

Session 1 — From Raw Files to Search Inputs Session 2 — Search Engines, Scoring & PSMs Session 3 — Protein Inference, FDR & Validation Session 4 — Mini Capstone: Search to Protein List

Session 1

Fee: Rs 8800

From Raw Files to Search Inputs

LC–MS/MS raw data formats and conversion concepts

vendor raw files (overview) mzML / mzXML / MGF ideas profile vs centroid data

Spectrum quality, charge states and precursor selection

isotope patterns and monoisotopic peaks charge state distribution simple spectrum QC ideas

FASTA databases and search space definition

UniProt / reference proteomes (concepts) contaminant and decoy entries (overview) enzyme, missed cleavages, mass windows

Session 2

Fee: Rs 11800

Search Engines, Scoring & PSMs

Search engine families and workflows (conceptual)

Mascot / Sequest / Andromeda (overview) MS-GF+, Comet and others (concepts) search parameter files

Peptide–spectrum matches and scoring logic

theoretical vs experimental spectra score, e value, expectation value ideas search tolerance and fragment mass error

Fixed and variable modifications in searches

carbamidomethyl Cys, oxidation Met phospho (concept only here) impact of too many variable mods

Session 3

Fee: Rs 14800

Protein Inference, FDR & Validation

Target–decoy strategy and FDR concepts

decoy generation ideas PSM, peptide and protein level FDR q values and score thresholds

Protein inference and grouping principles

unique vs shared peptides protein groups and leading proteins parsimony ideas

Validation and reporting of protein identification sets

1 percent FDR reporting conventions minimum peptide and PSM filters export formats for downstream tools

Session 4

Fee: Rs 18800

Mini Capstone: Search to Protein List

End to end walk through: from search setup to filtered identifications

Theory + Practical (guided)

Interpreting search result tables and QC plots (concepts)

score vs FDR curves peptide and protein counts missed cleavages and modification patterns

Deliverables: parameter sheet, filtered protein list and QC summary note

search parameter template exported peptide and protein tables one page QC and validation summary

PDF

Protein Identification & Database Search Training | Search Engines, Target–Decoy & FDR

Protein Identification — Database Search and FDR — Hands-on