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proteomics-quantification

Automate protein and peptide quantification from mass spectrometry data.

155|26|Updated Mar 14, 2026
Search Tags:#mass spectrometry#proteomics#quantification#LFQ#TMT#DIA
One-click install
npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-quantification
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: proteomics-quantification
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/proteomics/proteomics-quantification
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill proteomics-quantification

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

This Skill automates the process of quantifying protein and peptide abundance from mass spectrometry data, handling various experimental workflows like LFQ, TMT, and DIA. It standardizes the output across different methods, making downstream analysis more robust.

Core Features & Use Cases

  • Multiple Quantification Methods: Supports Label-Free Quantification (LFQ), Spectral Counting, and Intensity-Based Absolute Quantification (iBAQ).
  • Standardized Output: Generates consistent intensity matrices and reports regardless of the chosen method.
  • Use Case: You have raw peptide identification results from a mass spectrometry experiment and need to generate a protein abundance table for differential expression analysis. This Skill can process your data using your preferred quantification method (e.g., LFQ) and provide the necessary output.

Quick Start

Run the proteomics quantification skill using the provided demo data.

Frequently Asked Questions about proteomics-quantification

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

FAQPage Schema
How do I quantify protein abundance from mass spectrometry peptide data?▼

Protein quantification from mass spectrometry data is automated by processing input peptide sequences and intensities to generate normalized intensity matrices using LFQ, TMT, or DIA workflows.

Can I use DIA-NN and MaxQuant LFQ workflows for peptide quantification in the same pipeline?▼

Yes, both DIA-NN and MaxQuant LFQ workflows are supported alongside Skyline, standardizing peptide quantification outputs into consistent intensity matrices and yield metrics regardless of method.

What input data is required for label-free quantification of mass spectrometry data?▼

Accurate label-free quantification requires input peptide data containing both peptide sequence information and intensity values to properly calculate and normalize protein abundance matrices.

What is the difference between LFQ, TMT, and DIA workflows for protein quantification?▼

LFQ, TMT, and DIA represent distinct mass spectrometry acquisition and labeling strategies; this Skill standardizes their varied peptide intensity data into uniform protein abundance matrices.

Does this proteomics quantification method support iBAQ and spectral counting?▼

Yes, the Skill supports Label-Free Quantification, Spectral Counting, and Intensity-Based Absolute Quantification (iBAQ) to generate standardized protein abundance reports.

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