using-proteomics-skills

Using Proteomics Skills

This is the meta-skill that governs how all other proteomics skills are discovered, sequenced, and applied. Each specialized skill encodes the process an expert proteomics analyst would follow for one phase of work. This skill maps an incoming task to the right phase, routes to the corresponding skill, and keeps the overall analysis on track.

When a proteomics task arrives, identify the current phase and apply the corresponding skill. Do not improvise a phase that a dedicated skill already covers.

Skill Discovery

Route the task using the decision logic below:

• Don't know what the data is or which engine produced it yet? → reading-proteomics-data
• Have a matrix but unsure if samples/features are trustworthy? → performing-proteomics-quality-control
• Need to make samples comparable / stabilize variance? → normalizing-proteomics-data
• Missing values blocking a method that needs a complete matrix? → imputing-proteomics-data
• Suspect plate, instrument, or time-point bias? → correcting-proteomics-batch-effects
• Ready to test which proteins change between conditions? → performing-statistical-analysis
• Have a list of regulated proteins and need biological meaning? → interpreting-biological-results
• Need to synthesize results into a narrative or hypothesis? → formulating-biological-findings
• Writing or finalizing any analysis code? → applying-code-standards (cross-cutting)
• Implementing any of the above in Python? → analyzing-proteomics-data (use alphapepttools, cross-cutting)

If the request spans multiple phases (e.g. "run the full analysis"), follow the Lifecycle Sequence below in order.

Core Operating Behaviors

These behaviors apply at all times, across all skills. They are non-negotiable.

1. Surface Assumptions

Before implementing anything non-trivial, explicitly state your assumptions:

ASSUMPTIONS I'M MAKING:
1. [assumption about inputs — e.g. search engine, table type, intensity type]
2. [assumption about parameters or thresholds — e.g. completeness cutoff, FDR, fold-change]
3. [assumption about experimental design — e.g. groups, replicates, control vs. treatment]
→ Correct me now or I'll proceed with these.