Claude Skills by HolobiomicsLab

Use when you have native Thermo Fisher RAW mass spectrometry files and

Use when you receive raw MS data files from LC-MS, LC-IMS-MS, direct

Use when you have mass spectral libraries from multiple sources (e.g.,

Use when you have raw MRM sample files from an LC-MS/MS instrument and

Use when you have raw mass spectrometry data in one of the supported

Use when you have raw MS/MS spectra in one of the supported exchange

'Use when you have raw GC-MS output exported as CSV (containing columns:

Use when use this skill at the start of any mass spectrometry analysis

Use when when beginning a new mass spectrometry analysis workflow with

Use when you have multiple mzML or HDF5 feature tables from the same

Use when you have a set of ions already matched to a khipu instance (i.e.,

Use when you have mass spectrometry data available in multiple identifier

Use when you have raw or curated mass spectrometry data (MS1, MS2, or

Use when you have raw MS data files from supported instruments (Agilent,

Use when you have raw spatial metabolomics imzML files (paired with .ibd

Use when when raw MS/MS spectra from GNPS or similar databases contain

Use when when you have mass spectrometry data stored in non-standard

Use when you have raw mass spectrometry data in mzML or Bruker .d format

Use when you have received raw or vendor-converted centroid mzML files

Use when you have raw mass spectrometry data in CSV or mzML format and

Use when you have raw LCMS data in mzML or mzXML format from DDA, DIA,

Use when you have raw mass spectrometry data in vendor-specific formats

Use when when raw mass spectrometry spectral data has been imported into

Use when you have generated a complete feature table from mzML files

Use when you have a directory of mzML mass spectrometry files and need

Use when you need to store or retrieve mass spectrometry spectra (m/z

Use when after RAMClustR clustering and molecular weight inference via

Use when you have a normalized abundance matrix from LC-MS/MS profiling

Use when when you have received metabolomics mass-spectrometry data in

Use when when you have a mzPeak file (uncompressed ZIP archive containing

Use when you have converted multidimensional MS data (from Agilent .d,

Use when after feature extraction and peak recognition have produced

Use when when you have raw or processed TWIM-MS data (arrival time and

Use when when reproducing or validating a tandem mass spectrometry denoising

Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV)

Use when your input is a Pandas DataFrame containing mass spectrometry

Use when after applying retention time, abundance correlation, or EIC

Use when you have an unknown mass spectrum (or a representative metabolite

Use when you have raw or semi-processed MS/MS spectra in MSP format (e.g.,

Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited

Use when you have raw DDA, DIA (MS^E, AIF, SWATH-MS), or MS1-only mass

Use when you need to translate user-facing mass spectrometry query intent

Use when when you have raw ion mobility-mass spectrometry data (drift

Use when when you have preprocessed MS/MS spectral data (normalized peak

Use when when you have peak-detected LC-MS/MS data (MGF files with MS1

Use when after XCMS feature detection and alignment when you have a CSV-formatted

Use when after XCMS CentWave feature extraction when your feature table

Use when you have a peak table from LC-MS peak picking software (e.

Use when immediately after MZmine feature detection when you have both

Use when when you have processed LC-HRMS mzML files through a non-targeted