Foundations of Proteomics & Protein Bioinformatics — Hands-on

Build a rock-solid foundation in experimental proteomics and protein bioinformatics. Learn study design, sample preparation, MS data fundamentals, database searching with robust FDR control, essentials of quantitation and PTM interpretation, and produce reviewer-ready outputs.

Foundations of Proteomics & Protein Bioinformatics

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Session Index

Session 1 — Proteomics Study Design & Sample Prep Session 2 — MS Fundamentals, Raw Data & Formats Session 3 — Database Search, Scoring & FDR Session 4 — Quantitation, PTMs & Reporting

Session 1

Fee: Rs 12320

Proteomics Study Design & Sample Prep

Experimental design & controls

biological/technical replicates randomization & blocking power & depth

Sample prep & digestion

lysis & cleanup reduction/alkylation trypsin/LysC

Separation & enrichment basics

LC gradients fractionation PTM enrichment (Phospho/Glyco)

Session 2

Fee: Rs 16520

MS Fundamentals, Raw Data & Formats

Ionization & analyzers

ESI Orbitrap/Q-TOF DDA/DIA

Spectra & metadata

MS1/MS2 isotopes/charge states instrument settings

Open formats & QC

mzML/mzXML/MGF QC metrics (ID rates, TIC) FAIR data

Session 3

Fee: Rs 20720

Database Search, Scoring & FDR

Search engines & params

Comet/MS-GF+/X!Tandem precursor/fragment tol. fixed/variable mods

Target–decoy & validation

PSM/peptide/protein FDR q-values rescoring (Percolator)

Databases & proteotypic peptides

UniProt/Swiss-Prot contaminants/decoys enzyme rules/missed cleavages

Session 4

Fee: Rs 26320

Quantitation, PTMs & Reporting

Label-free & isobaric basics

intensity/ion count TMT/iTRAQ concepts normalization & batch

PTM calling & localization

localization scores site-level FDR motifs & biology

Reproducible outputs

report templates figure panels data & method checklists

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Foundations of Proteomics & Protein Bioinformatics Training | Study Design, MS Basics, Search & FDR, Quant & PTMs

Foundations of Proteomics & Protein Bioinformatics — Hands-on