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Validate Orbitrap mass spectrometry data by verifying instrument metadata and quantifying fragment ion signal-to-noise ratios.
This skill provides a rigorous protocol for validating raw Orbitrap mass spectrometry spectral data. It ensures that the instrument operated within expected parameters (resolving power, AGC injection time) and that observed peptide fragment ions are significantly above the noise floor.
Apply this skill when you have extracted a raw Orbitrap scan from a .raw file and need to verify spectral quality before proceeding to peptide identification or quantification workflows.
rawrr R package to extract metadata and calculate signal-to-noise ratios for specific peptide fragments.Scientific AI agents with access to R environments and the rawrr package, particularly those working in bioinformatics or proteomics.
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GitHub Actions Workflow Inspector
Verify and locally reproduce GitHub Actions CI workflows to validate badge status and build integrity.
Injection Sequence Annotation
Identifies and validates QCpool sample spacing in Sciex Multiquant metabolomics/lipidomics exports.
PyTorch Pretrained Weight Loader
Load pretrained PyTorch model checkpoints to rank candidate molecules or score spectra in metabolomics without retraining.
Positional Encoding for Spectral Sequences
Embeds sequential information into mass spectrum m/z-intensity pairs for transformer-based MS/MS interpretation in IDSL_MINT.
Record Field Transformation & Collation
Transform and collate tabular records into structured JSON dictionaries using field mapping, filtering, and grouping for scientific metadata.
Fragmentation Spectrum Extraction
Extract and deconvolve individual fragmentation spectra from composite mass spectrometry data for metabolomics and exposomics annotation.
Metabolomics QC Report Generation
Automates the export of LC-MS metabolomics quality control results into publication-ready plots, HTML reports, and data tables.
GNPS Molecular Network Metadata Organization
Fetch, extract, and standardize GNPS molecular networking job archives for NPLinker integration.
Metabolomic Feature Table Imputation
Replace zero and missing values in LC-MS metabolomics feature tables using minimum-value-based interpolation.
LC Gradient Vector Encoding & Decoding
Convert LC gradient parameters into normalized numerical vectors for Bayesian optimization and GP regression.
Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
ToolUniverse Gateway
Unified agent gateway to 1000+ scientific tools (bioinformatics, drug discovery, genomics) via Harvard's ToolUniverse, returning JSON for downstream workflows.
CTX Link Check — Documentation Link Auditor
Scan project markdown for broken internal links, missing images, and unreachable external URLs; produce a clear report and suggested fixes before docs releases.
MatchMS (mass spectrometry processing)
Mass spectrometry data processing: import/export mzML/MGF/MSP, filter and normalize spectra, compute spectral similarity (cosine/modified cosine), and build rep
Skill Evolve
Iteratively improve an existing Agent Skill by observing real outputs, extracting recurring failure patterns, and applying small, verifiable fixes (OTF + JIT +
matchms — Mass Spectrometry Processing
Python library skill for importing, filtering, and comparing mass spectra (mzML/MGF/MSP); builds reproducible preprocessing pipelines and computes spectral simi
MatchMS — Mass Spectrometry Utilities
Import, process and compare mass spectrometry spectra (mzML/MGF/MSP) with filters, similarity metrics and reproducible pipelines for metabolomics workflows.
KEGG Pathway Enrichment (clusterProfiler)
Run KEGG pathway and module enrichment using clusterProfiler (enrichKEGG/enrichMKEGG) to find metabolic and signaling pathways over-represented in a gene list.