Which file formats does this skill support?

It supports a wide range of formats including mzML, mzXML, FASTA, pepXML, protXML, and mzIdentML for comprehensive experimental data handling.

How do I install the required library for this skill?

You can install the library using 'uv pip install pyopenms' or standard pip to enable the underlying functionality required by this skill.

What is PyOpenMS used for?

PyOpenMS provides Python bindings for the OpenMS library, used for computational mass spectrometry tasks like protein identification, metabolite quantification, and signal processing.

Does it integrate with standard Python data science tools?

Absolutely, it allows for seamless export of mass spectrometry data structures to Pandas DataFrames and NumPy arrays for advanced statistical analysis.

Can I use this for metabolomics workflows?

Yes, it includes specific capabilities for untargeted metabolomics, including feature detection, retention time alignment across samples, and database annotation.

PyOpenMS Analysis

Name: PyOpenMS Analysis
Author: Microck

byMicrock

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Data Science & ML

Facilitates mass spectrometry data analysis using the pyOpenMS library for proteomics and metabolomics workflows.

About

PyOpenMS Analysis is a specialized capability for Claude that streamlines the processing and interpretation of complex mass spectrometry data. It provides expert guidance on using the Python bindings for the OpenMS library, covering the entire pipeline from raw data ingestion (mzML, FASTA) and signal processing to feature detection, peptide identification, and metabolomics quantification. This skill is ideal for researchers and bioinformaticians looking to automate LC-MS/MS workflows, integrate with pandas/NumPy for downstream analysis, and implement best practices in computational mass spectrometry within their coding environment.

Key Features

Feature detection and linking algorithms for quantitative proteomics
Spectral signal processing including smoothing, filtering, and centroiding
81 GitHub stars
Specialized metabolomics preprocessing and retention time alignment
Peptide and protein identification workflows with FDR filtering support
Comprehensive file I/O for formats like mzML, mzXML, FASTA, and mzIdentML

Use Cases

Building automated LC-MS/MS data processing pipelines for high-throughput experiments
Developing untargeted metabolomics tools with automated feature mapping and annotation
Identifying peptides and proteins from complex identification files using various search engines

About

Key Features

Feature detection and linking algorithms for quantitative proteomics
Spectral signal processing including smoothing, filtering, and centroiding
81 GitHub stars
Specialized metabolomics preprocessing and retention time alignment
Peptide and protein identification workflows with FDR filtering support
Comprehensive file I/O for formats like mzML, mzXML, FASTA, and mzIdentML

Use Cases

Building automated LC-MS/MS data processing pipelines for high-throughput experiments
Developing untargeted metabolomics tools with automated feature mapping and annotation
Identifying peptides and proteins from complex identification files using various search engines