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sdrf:techrefine

Refine and verify SDRF technical metadata from raw mass spectrometry files.

11|9|Updated Mar 18, 2026
Search Tags:#proteomics#modifications#instrument#raw-data#sdrf#techsdrf#mass-tolerance
One-click install
npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-techrefine
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: sdrf:techrefine
Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-techrefine
Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-techrefine

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Proteomics SDRF files often contain inaccurate or missing technical metadata because these details are manually entered from publications or PRIDE records.

Core Features & Use Cases

  • Automated refinement: Leverages the techsdrf tool to detect instrument models, tolerances, acquisition mode, and modifications directly from raw mass‑spectrometry files.
  • Multiple input options: Works with PRIDE PXD accessions, local raw file directories, or SDRF‑only inspection.
  • Guided correction: Generates a refined SDRF, highlights mismatches, and lets the user approve each change.

Quick Start

Ask the assistant to run the /sdrf:techrefine skill on your SDRF file and associated raw MS data to obtain a refined SDRF.

Frequently Asked Questions about sdrf:techrefine

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I validate SDRF technical metadata from raw mass spectrometry files?▼

You can validate SDRF technical metadata by using the techsdrf command-line tool to detect instrument models, mass tolerances, modifications, and acquisition mode directly from raw MS files. This generates a refined SDRF with mismatch highlights for approval.

Why does my proteomics SDRF file contain inaccurate instrument parameters?▼

Proteomics SDRF files often contain inaccurate technical metadata because these details are manually entered from publications or PRIDE records. Automated refinement using raw mass spectrometry files verifies actual instrument parameters against the documented metadata.

Can I refine SDRF metadata using a PRIDE PXD accession instead of local files?▼

Yes, you can refine SDRF metadata using a PRIDE PXD accession, a local directory of raw files, or SDRF-only inspection. The tool fetches the necessary raw mass spectrometry data to validate technical parameters.

Do I need raw file converters to validate mass tolerance and modifications in SDRF?▼

Yes, validating mass tolerance and modifications requires appropriate raw file converters like ThermoRawFileParser or msconvert, alongside the techsdrf command-line tool, to parse raw mass spectrometry files and extract technical metadata.

What is the best way to detect acquisition mode and instrument models from raw MS data?▼

The best way to detect acquisition mode and instrument models is using the techsdrf tool, which analyzes raw mass spectrometry files to automatically extract and verify these technical parameters, generating a corrected SDRF for your proteomics dataset.

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