Individual skill

reading-proteomics-data

Read proteomics search engine outputs (PSM tables, protein matrices) from search engines like DIA-NN, MaxQuant, Spectronaut, AlphaDIA, MSFragger, Sage. Use for ingesting data, mapping columns to standard names, and initial filtering.

plugins/proteomics/skills/reading-proteomics-data/SKILL.md

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Last checked: Nov 6, 2026

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Repository stars (not skill ratings): 17
Repository last updated: Oct 14, 2026
License: Apache-2.0

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agent-skills Repository topic
proteomics Repository topic
data Derived category

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references/psm-columns.mddoc · 4,513 bytes

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# Reading Proteomics Search Engine Outputs

## 1. Context

### Table Types

| Type                                   | Format                    | Feature level                                              | Use When                                         |
| -------------------------------------- | ------------------------- | ---------------------------------------------------------- | ------------------------------------------------ |
| **Peptide spectrum match (PSM) table** | Long (one row per match)  | Precursor, Peptides (optional), Proteins, Genes (optional) | Peptide-level analysis, PTMs, custom aggregation |
| **Protein Group (PG) matrix**          | Wide (proteins × samples) | Proteins, Genes (Optional)                                 | Protein-level analysis                           |

**Use PG matrices** for protein- and gene-level analyses, if available

### Engine Detection Signatures