pyopenms
Category: life-sciences · License: 3 clause BSD license · Version: 2.1 · Includes scripts
Tags: mass spectrometry, proteomics, metabolomics, LC-MS, bioinformatics
When to use it
Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.Example requests
Ask your agent in plain language, for example:- “How do I run untargeted feature detection on a DDA mzML file in Python?”
- “I have 12 plasma metabolomics runs (QC_01.mzML … S10.mzML) from a Q Exactive in positive mode. I need a samples-by-features intensity table across all runs. My old script calling FeatureFinder(‘centroided’) now crashes after I upgraded to pyopenms 3.5. Can you fix this and also group adducts like [M+Na]+ with [M+H]+ before annotating against HMDB?”
- “I ran a database search on my tryptic HeLa digest and got an idXML file. I want to rescore it, keep only peptide hits at 1% FDR, and make sure each spectrum only keeps its best hit. I also have the FASTA I searched against.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.