Claude Skills by HolobiomicsLab

Use when you have a Cardinal MSImagingExperiment object (e.g., from imzML

Use when when you have raw mzML files from LC-MS/MS metabolomics experiments

Use when you have raw mzML mass spectrometry data and need to detect

Use when after raw data processing and feature extraction (e.g., via

Use when after aligning raw mass spectra into a 2D feature intensity

Use when you have (1) aligned LC-MS/MS feature quantification matrix

Use when after LC-MS feature clustering based on MS-DIAL peak character

Use when when you have an untargeted metabolomics dataset with MS2 fragmentation

Use when you have vendor-independent centroided mzML files from LC- or

Use when after running qiime qemistree make-hierarchy and obtaining a

Use when you have vendor raw mass spectrometry data files (.raw) from

Use when you have raw MS data files in vendor-native format (.raw, .d,

Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g.,

Use when you have raw MS/MS spectral data in one or more standard mass

Use when you have uploaded MS/MS data to MassIVE with validated sample-information

Use when you have raw or semi-processed mass-spectrometry peak data from

Use when after MSConvert has converted vendor-specific raw mass spectrometry

Use when when you have mass spectrometry spectra in one of the six supported

Use when you have mzML or mzXML mass spectrometry data files and need

Use when you have experimental fragment m/z peaklists from Q-Exactive

Use when you are generating synthetic LC-MS/MS data for method validation,

Use when you have preprocessed MS/MS spectral data (in positive or negative

Use when when building a re-usable spectral reference library for lipidomics

Use when after loading a pixel array (NumPy format) and its associated

Use when you have raw or preprocessed single-channel (2D array) or multi-channel

Use when you have paired .imzML (XML metadata) and .

Use when you have raw MS imaging data in imzML (continuous or processed)

Use when when you have preprocessed MALDI-MSI data (in msimat format)

Use when you have raw or preprocessed MS imaging data archived as an

Use when you have raw or processed MSI data (in imzML or rMSIproc formats)

Use when you have raw mass spectrometry imaging data (2D or 3D spatial

Use when you have raw line-scan MSI data from a vendor instrument (Agilent,

Use when your input mass spectrometry imaging data is in a proprietary

Use when you have raw mass spectrometry data from an instrument not yet

Use when when correcting LC-MS fractional abundances of measured isotopologues

Use when mS quantification data exhibits intensity drift—a systematic

Use when when you have a metabolite structure (SMILES or molecular graph)

Use when when you have a feature table from LC-MS preprocessed data (e.g.

Use when when preprocessing a public MS/MS spectral library (e.g., GNPS)

Use when you have a large MS/MS experiment (mzML format) requiring lipid

Use when when you have an unknown MS/MS spectrum (with ≥10 peaks, precursor

Use when you have a set of unidentified tandem mass spectra (queries)

Use when when you have an unknown MSMS spectrum (precursor m/z and fragment

Use when when you have detected peaks in a direct injection FTICR-MS

Use when when extracting and validating chromatographic peaks for target

Use when you have a GC-MS dataset with a Match.Factor column (output

Use when when you need to create negative control or background-only

Use when you plan to perform repeated queries or filtering on MS metadata

Use when you have peak/feature tables from one or more of MZmine, XCMS,

Use when when integrating LC-MS/MS data from diverse sources (e.g., public