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bio-metabolomics-metabolite-annotation

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.

OpenClawNanoClaw分析处理复现实验bio-metabolomics-metabolite-annotation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — proteomics & metabolomicsmetabolite

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-metabolomics-metabolite-annotation

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • features <- read.csv('feature_table.csv')。
  • search_hmdb <- function(mz，adduct = '[M+H]+'，ppm = 10) { # Calculate neutral mass ，面向 m/z adduct_masses <- list( '[M+H]+' = 1.007276，'[M+Na]+' = 22.989218，'[M-H]-' = -1.007276，'[M+Cl]-' = 34.969402 )。
  • neutral_mass <- mz - adduct_masses[[adduct]]。
  • # Query HMDB (或 local database) # Returns putative matches matches <- QueryHMDB(neutral_mass，ppm) return(matches) }。

原始文档

SKILL.md 摘录

Database Matching by m/z

Goal: Generate putative metabolite identifications by matching observed m/z values against HMDB.

Approach: Convert m/z to neutral mass by subtracting adduct mass, then query HMDB within a specified ppm tolerance.

"Annotate my metabolomics features with compound identities" → Match detected features against metabolite databases by exact mass, MS/MS spectra, and retention time to assign compound identities with confidence levels.

library(MetaboAnalystR)

## Apply to all features

annotations <- lapply(features$mz, function(m) search_hmdb(m, '[M+H]+', 10))

MS/MS Spectral Matching

from matchms import calculate_scores
from matchms.importing import load_from_mgf
from matchms.similarity import CosineGreedy

适用场景

  • 适合在assigning compound identities to detected features in untargeted metabolomics时使用。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • xcms-preprocessing - Generate feature table
  • pathway-mapping - Map annotated metabolites to pathways
  • proteomics/spectral-libraries - Similar spectral matching concepts

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