Individual skill
proteomics-pro
Mass-spectrometry proteomics — experimental design, data processing, quantification, and functional interpretation.
skills/proteomics-pro/SKILL.md
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## Overview
proteomics-pro covers mass-spectrometry-based proteomics from experimental design to biological
interpretation: sample preparation, LC-MS/MS acquisition strategies (DDA, DIA, targeted), database
searching, quantification (label-free, TMT/iTRAQ, SILAC), and downstream analysis including
differential expression, PTM analysis, and pathway enrichment.
Proteomics data is noisier and more incomplete than transcriptomics — missing values are the norm,
dynamic range spans orders of magnitude, and peptide-to-protein inference is genuinely ambiguous.
This skill emphasizes designs and statistics that are robust to those realities.
## When to use
- Designing a proteomics experiment: DDA vs DIA vs targeted (PRM/MRM), labeling strategy,