Claude Skills by HolobiomicsLab

Use when augmenting mass spectrometry ion images in ISO mode (isotope

Use when when you need to create synthetic noisy MS/MS spectra from clean

Use when processing raw MS intensity tables from long measurement sequences

Use when you have an MS/MS peak list and need to remove electronic noise—specifically

Use when when working with raw or filtered MsmsSpectrum objects where

Use when after noise reduction when working with imported imzML MSI data

Use when you have processed LC-MS data (mzML or vendor format) and need

Use when when you have loaded aligned peak data (from a preceding molecular

Use when you have loaded a raw or partially processed MsmsSpectrum object

Use when your lipidomics experiment includes spiked internal lipid standards

Use when you have raw mass spectrometry intensity measurements from sample

Use when after peak recognition has identified features (m/z and retention

Use when you have extracted mass tracks (EICs) from multiple LC-MS samples

Use when after applying batch correction (e.g., via pycombat) to a multi-batch

Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap

Use when after instantiating a specXplore dashboard session layer with

Use when you have NMR metabolomics measurements paired with pre-analytical

Use when when you have a web-based visualization of aligned mass spectrometry

Use when you have omics statistical results (p-values, effect sizes,

Use when your mass spectrometry DataFrame contains m/z, retention time

Use when when you have extracted ion chromatograms (XICs), ion mobilograms

Use when after structural clustering (isotopologue grouping, adduct detection,

Use when when you have a high-resolution mass spectrometry dataset with

Use when you have mass spectrometry data (chromatograms, spectra, peak

Use when after LC-MS data has been converted to mzML format and processed

Use when when you have loaded extracted ion chromatogram traces (via

Use when you have resolved USI (Unified Spectrum Identifier) spectrum

Use when after normalizing a featuredata matrix (samples × metabolites),

Use when you have loaded m/z and intensity arrays from an MZA file (via

Use when when you have mass spectrometry data in a Pandas DataFrame with

Use when you have validated omics data loaded into R (expression matrices,

Use when after loading a LA-ICP-MS image into pew², you need to isolate

Use when when you have computed PCA coordinates from chemical annotation

Use when after msFeaST pipeline execution has produced a dashboard_data.json

'Use when after automated peak detection has identified candidate peaks

Use when after running saturation repair or multidimensional smoothing

Use when after building a SummarizedExperiment from metabolomics data

Use when after building a SummarizedExperiment object containing LC-MS

Use when you have processed LC-MS run data (feature table or peak detection

Use when you have added a known internal standard compound to your nano-DESI

Use when you have lipidomics data from LipidSearch or LIQUID output that

Use when after isotope correction has been applied to MSI ion images,

Use when your metabolomics dataset includes internal standard metabolites

Use when you have preprocessed metabolomics data with multiple candidate

Use when you have loaded processed LC-MS data (mzML or vendor format)

Use when after batch correction of metabolomics QC samples using pooled

Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled

Use when you have (LC-)IM-MS lipidomics data from samples spiked with

Use when your IM-MS lipidomics samples have been spiked with fully labeled

Use when when a new file format specification exists as a living document