Post-Translational Modifications (PTM) Analysis — Hands-on

Specialize in post translational modification (PTM) proteomics workflows. This module covers PTM biology, enrichment strategies, LC–MS/MS acquisition concepts, search parameter setup with variable modifications, site localization and quantitative analysis that links dynamic PTM changes to pathways and phenotypes.

Post-Translational Modifications (PTM) Analysis

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Session Index

Session 1 — PTM Biology & Experiment Planning Session 2 — PTM Enrichment Strategies & Sample Prep Session 3 — PTM Search Setup, Site Localization & FDR Session 4 — Quantitative PTM Analysis & Mini Capstone

Session 1

Fee: Rs 8800

PTM Biology & Experiment Planning

Overview of major PTM classes and biological roles

phosphorylation acetylation ubiquitination and others (concepts)

Choosing PTM targets and biological questions

signaling pathways and kinases time course and stimulus response sample type constraints (cells, tissues, biofluids)

Experimental design for PTM focused proteomics

controls and treated groups replicates and spike in standards (concepts) choice of label free vs isobaric tags

Session 2

Fee: Rs 11800

PTM Enrichment Strategies & Sample Preparation

PTM enrichment concepts for low stoichiometry marks

phosphopeptide enrichment overview antibody based pulldown ideas affinity materials and selectivity

Popular phospho enrichment workflows (concept level)

IMAC and TiO2 ideas single vs multi step enrichment washing and elution strategies

Sample preparation considerations for PTM stability

inhibitors during lysis protein digestion conditions loss and bias awareness

Session 3

Fee: Rs 14800

PTM Search Setup, Site Localization & FDR

Search parameters for PTM rich datasets (conceptual)

variable modification settings neutral loss behavior (high level) enzymes and missed cleavages

PTM site localization scores and probabilities

localization score concepts site probability thresholds classifying class I and lower confidence sites

FDR, decoys and validation in PTM data sets

target decoy thinking for PTM searches site level vs PSM level FDR ideas exporting localized PTM tables

Session 4

Fee: Rs 18800

Quantitative PTM Analysis & Mini Capstone

Quantitative analysis of PTM site intensities

Theory + Practical (guided workflow)

Motif, kinase and pathway level interpretation concepts

motif enrichment ideas linking sites to kinases (concepts) pathway and network mapping overview

Mini capstone: from localized PTM table to regulated site list

QC of PTM intensities hit list of regulated sites short biological interpretation summary

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Post-Translational Modifications (PTM) Analysis Training | Enrichment, Site Localization & Quantitative PTM

Post-Translational Modifications (PTM) Analysis — Hands-on