Claude Skills by HolobiomicsLab

Use when when you have a raw or partially processed MS/MS spectra collection

'Use when you have raw LC-MS/MS data in mzML or mzXML format and need

Use when you have MGF or native MS/MS arrays (mz_array, intensity_array,

'Use when when you have a GC-MS dataset (CSV with columns: Component.RT,

Use when when comparing two or more MS/MS spectra for compound identification,

Use when you have raw or parsed tandem MS spectra (MGF, mzML, or in-memory

Use when after computing a sparse pairwise distance matrix from nearest

Use when you need to determine the complete set of validated instrument/vendor

Use when you have high-resolution MS1 data (mzXML, mzML, or netCDF format)

Use when when you have loaded raw MS1 data from multiple instrument formats

Use when you have FIA-MS, LC-MS, or GC-MS full-scan data in mzML format

Use when when you have an LC-HRMS feature table (with m/z values, retention

Use when you have merged MS1 spectra (output from spectral binning/merging

Use when when you have raw LC-MS data files and need to identify which

Use when when you need to prototype, test, or benchmark MS1-only acquisition

Use when you have a Thermo Fisher Scientific .raw file from an Orbitrap

Use when you have (1) a peaklist from untargeted LC/HRMS analysis with

Use when when you need to generate synthetic LC-MS/MS data to test fragmentation

Use when after generating a scan index from a Thermo Fisher Orbitrap

Use when after GNPS spectral library search has returned matched chemical

Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that

Use when you have MS2 tandem mass spectrometry data in .mzML format and

Use when you have centroided MS2 spectra from data-dependent LC- or GC-HRMS

Use when after aligning MS2 fingerprints across samples (generating a

Use when after MS2 fingerprints have been generated by counting MS2 peaks

Use when you have two MemoMatrix objects generated from separate sample

Use when you have LC-MS/MS data in mzML, mzXML, or MGF format from one

Use when you have extracted MS/MS spectra for a given metabolomic feature

Use when you have data-dependent acquisition (DDA) MS2 spectra from HRMS

Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp,

Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and

Use when when you have a resolved spectrum file in mzML or mzXML format

Use when when beginning a MEMO analysis workflow with raw or unaligned

Use when after concatenating replicate MS/MS spectra for each precursor

Use when you have acquired LC-IMS-MS/MS data (or equivalent multidimensional

Use when you have MS2 fragmentation spectra from multiple metabolomics

Use when you have LC-MS/MS metabolomics data in MGF format and need to

Use when you have extracted an MS1 feature table (from XCMS or custom

'Use when after frequency-based denoising of MS/MS spectra, when you

Use when you have two or more LC-MS/MS datasets (in mzML, mzXML, or MGF

Use when after temporal intensity profile correlation and exact mass

Use when you have DDA LC-MS/MS raw data (mzML format) with detected chromatographic

Use when after sample alignment and feature grouping steps in untargeted

Use when when you have DDA LC-MS/MS data (mzML format) with identified

Use when you have DDA (data-dependent acquisition) LC-MS/MS data with

Use when you have raw or unstructured MS2 spectral data (from untargeted

Use when when you have raw MS2 spectra (m/z and intensity pairs) and

Use when after creating a GNPS mass spectral molecular network and running

Use when you have a GNPS-generated molecular network (either classical

Use when when you have a GNPS molecular network (classical or feature-based)