Shotgun Proteomics and LC–MS Workflows — Hands-on

Learn how to turn prepared peptide samples into high quality discovery proteomics data using LC–MS/MS. This module focuses on shotgun proteomics workflows, from LC gradient design and DDA acquisition methods to run-order planning, QC injections and basic performance checks for robust protein identification and quantitation.

Shotgun Proteomics and LC–MS Workflows

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Session Index

Session 1 — Shotgun Proteomics Concepts & Workflow Design Session 2 — LC Setup, Gradients & Chromatography Session 3 — DDA Acquisition Methods & Run QC Session 4 — Mini Capstone: LC–MS Run Plan & Checklist

Session 1

Fee: Rs 8800

Shotgun Proteomics Concepts & Workflow Design

Shotgun proteomics overview and data dependent workflows

complex peptide mixtures DDA vs DIA (high level) discovery vs targeted follow up

Linking sample prep to LC–MS method choices

load amount decisions gradient length vs depth number of samples vs run time

High level workflow map for a discovery proteomics study

sample prep to raw data QC injections basic analysis outline

Session 2

Fee: Rs 11800

LC Setup, Gradients & Chromatography

LC plumbing and nanoLC column basics (conceptual)

trap and analytical configuration particle size and column length backpressure and flow rate

Gradient design for complex peptide separations

mobile phases A/B loading, washing and elution segments short vs long gradients

Chromatographic quality indicators and basic troubleshooting

peak shape and tailing retention time stability carryover reduction strategies

Session 3

Fee: Rs 14800

DDA Acquisition Methods & Run QC

DDA method structure and key parameters (conceptual)

survey MS1 scan top N selection dynamic exclusion logic

Isolation windows, collision energy and charge state filters

isolation width choices normalised collision energy concepts include and exclude lists (overview)

Run level QC metrics and simple dashboards (conceptual)

identification counts trend RT alignment of standards instrument stability checks

Session 4

Fee: Rs 18800

Mini Capstone: LC–MS Run Plan & Checklist

End to end run order planning with blanks, standards and samples

Theory + Practical (planning exercise)

Creating an LC–MS method and QC summary sheet (template based)

gradient and method summary QC sample placement acceptance criteria outline

Deliverables: run plan, checklist and simple QC tracking template

run-order table method one page summary QC log sheet

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Shotgun Proteomics and LC–MS Workflows Training | DDA LC–MS/MS Methods & Run QC

Shotgun Proteomics and LC–MS Workflows — Hands-on