Claude Skills by HolobiomicsLab

Use when when preparing raw MS2 spectra (m/z and intensity pairs) for

Use when when you have extracted a raw Orbitrap scan from a .raw file

Use when after MS1 extraction (coarse/fine error correction, EIC window

Use when you have raw spectroscopic datasets (NMR, HSQC, COSY, IR) in

Use when you have multi-sample MS1 data (from Agilent, Thermo, Bruker,

Use when you have a query mass spectrum (or representative metabolite

Use when after peak picking and alignment have been performed on preprocessed

Use when after running annotateRC to generate ranked candidate annotations

Use when when you have pre-computed dense embeddings for query spectra

Use when when you have identified a spectral window of interest in a

Use when you have real LC-MS/MS data (mzML) from a complex sample (e.g.,

Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from

'Use when you have executed multiple database search pipelines (Dereplicator,

Use when when you need to understand or modify how MS2Query routes query

Use when when you have implemented or obtained a spectral library search

Use when when you have executed batch searches of MS/MS spectra against

Use when you have mzML mass spectrometry data and a list of predicted

Use when after inferring Mass2Motif definitions from LDA modeling when

Use when when you have processed LC-MS/MS spectral data in .mgf format

Use when when you have computed a sparse pairwise distance matrix from

Use when when you have experimental MS/MS spectra (from mzML or .rda

Use when after extracting and optionally combining MS2 spectra from a

Use when after preprocessing and filtering mass spectra (peak filtering,

Use when you have MSMS spectra from two or more compounds and need to

Use when after clustering peak networks from INADEQUATE spectra and before

Use when when you have detected LC-MS/MS features (MS1 peaks with MS2

Use when after acquiring MS/MS spectral data from untargeted metabolomics

Use when after feature detection and alignment across LC-MS/MS runs (via

Use when when you have paired MS/MS spectra (unknown and known metabolites)

Use when use when the workflow requires spectral-similarity-prediction-evaluation.

Use when when you have paired MS/MS spectra with known structural similarity

Use when you have a query MS/MS spectrum and need to identify the -matching

Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml,

Use when after discovering Mass2Motifs via LDA topic modeling on MS/MS

Use when when you have extracted MS2 spectra from DDA chromatographic

Use when you have a query spectrum (or set of query spectra) and need

Use when you have a collection of preprocessed and cleaned mass spectrometry

Use when you have a query electron ionization (EI) mass spectrum and

Use when after generating TP candidates (via in-silico prediction or

Use when you have an unknown query spectrum suspected to carry a post-translational

Use when when you have extracted low-resolution mass spectra from individual

Use when after training a Word2vec model on tokenized mass spectra and

Use when when you have raw mass spectra in an MSImagingArrays object

Use when when you have pre-trained embedding vectors (e.g., from MSBERT)

'Use when when preparing MS/MS spectra from .msp files for transformer-based

Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown

Use when when you need to prepare mass spectra and molecular structures

Use when when you have a collection of normalized mass spectrometry spectra

Use when when converting pre-processed MS/MS spectra into fixed-length

Use when when you have a set of mass spectra (query or library) that