# Bioconductor Mzid

A parser for mzIdentML files implemented using the XML package.

- Repository: https://github.com/bioMate-AI/biomate-bioconductor-kb (793 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-06-20
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mzid -g -a claude-code -y`
Codex: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mzid -g -a codex -y`
Cursor: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mzid -g -a cursor -y`
Gemini CLI: `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-mzid -g -a gemini-cli -y`

## Description

A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less 'pretty' output than a vendor specific parser. Please contact th

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# mzID

## Dependencies & Environment

> Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

- **Version:** 1.50.0 · **Bioconductor:** 3.23 · **R:** ≥ 4.6
- **Imports:** XML, plyr, doParallel, foreach, iterators, ProtGenerics
- **System requirements:** URL
- **Install:** `BiocManager::install("mzID")`

## When to Use
- **Parsing mzIdentML Files**: Reading HUPO-PSI standard `mzIdentML` (.mzid) files containing peptide and protein identification results using the `mzID()` function.
- **Data Flattening**: Converting complex, nested structures of mzIdentML files into flat, easy-to-manipulate R `data.frame` objects using the `flatten()` function.
- **Metadata Extraction**: Extracting search database details, peptide-spectrum matches (PSMs), and search engine scores for downstream custom analysis.

## When NOT to Use
- For parsing raw mass spectrometry spectra (mzML, mzXML) or quantitative data (mzQuantML), use `mzR` instead because `mzID` only parses identification files.
- For high-level quantitative proteomics data manipulation, use `MSnbase` instead because `mzID` is strictly a barebones parser for identification data.

## Data Requirements
- **Input**: Valid `mzIdentML` (.mzid) files conforming to the HUPO-PSI schema.
- **Structure**: The parsed `mzID` object contains slots for `parameters`, `psm`, `peptides`, `evidence`, and `database`.

## Key Parameters
- **file**: Path to the mzIdentML file to be parsed (passed as the first argument to `mzID()`).

The rest: https://github.com/bioMate-AI/biomate-bioconductor-kb/blob/HEAD/skills/proteomics/mzid/SKILL.md