Capstone — End to End Proteomics Project — Hands-on

Use this capstone to consolidate all concepts from the proteomics track into a single end to end project. You will walk through study framing, sample and QC planning, search and quant thinking, result review and biological storyboarding, ending with a publication style report outline and checklist.

Capstone — End to End Proteomics Project

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Session Index

Session 1 — Project Briefing and Study Blueprint Session 2 — Workflow Sketch, Search and Quant Plan Session 3 — QC Review, Result Frames and Biology Session 4 — Final Storyboard, Report and Checklist

Session 1

Fee: Rs 8800

Project Briefing and Study Blueprint

Project context, question and biological system on paper

defining the comparison or time course selecting sample types and matrices linking to a simple biological hypothesis

High level experimental design and power thinking

grouping and replication ideas blocking and randomization concepts sources of variation and confounding

Blueprint of samples, runs and files for the project

sample inventory and ID map expected number of injections simple run order and plate sketch

Session 2

Fee: Rs 11800

Workflow Sketch, Search and Quant Plan

End to end workflow sketch from sample to tables

sample prep and LC MS idea blocks search, FDR and quant steps report generation on the right side

Database, modifications and search parameter choices

organism and contaminant concepts fixed and variable modification ideas FDR targets at PSM and protein level

Quantitative layer and normalization plan on paper

choice of label free or isobaric view normalization and batch correction ideas intended comparisons and contrasts

Session 3

Fee: Rs 14800

QC Review, Result Frames and Biology

Thinking through QC checks for the capstone project

system suitability and ID rate views sample level missingness patterns principal component and batch signals

Designing result tables and figures conceptually

summary table of key proteins volcano and heatmap ideas simple pathway or network diagrams

Linking the proteomics findings back to biology

connecting markers to pathways alternative explanations and caveats ideas for validation experiments

Session 4

Fee: Rs 18800

Final Storyboard, Report and Checklist

Storyboard of the full project from question to conclusion

theory plus storyboard worksheet

Outline of a publication style methods and results section

sections for samples and LC MS search, FDR and quant description figures and tables placement ideas

Capstone checklist for end to end proteomics projects

design, QC and analysis items data deposition and metadata notes common pitfalls and reminder list

PDF

Capstone — End to End Proteomics Project Training | Full Workflow Design and Reporting

Capstone — End to End Proteomics Project — Hands-on