Claude Skills by HolobiomicsLab

Use when you have multiple CSV files containing feature-by-sample matrices

Use when after peaks have been assigned to heteroatom classes (e.g.,

Use when after running inference on a trained structure prediction model

Use when after peak detection and MS1 feature extraction from FIA-MS,

Use when after MS1 feature detection and spectra merging in an untargeted

Use when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS,

Use when adopting a mass spectrometry-based analysis tool (e.

Use when you have preprocessed metabolite intensity data (log2-transformed,

Use when after computing PLAGE-derived activity scores for pathways or

Use when you have an LC-MS peak-intensity matrix with observed m/z values

Use when after computing a histogram of all pairwise mass differences

Use when you have a trained formula ranking model (such as MIST-CF) and

Use when after accurate mass searching has assigned multiple detected

Use when you have a characterized lipid species (with defined class and

Use when when you have unidentified LC/MS features (m/z, retention time,

Use when after temporal correlation has identified candidate feature

Use when when initializing an mWISE annotation pipeline with a new or

Use when when you have derivatized metabolite structures (SMILES or mol

Use when when you have binned mass spectrometry imaging peaks and want

'Use when when annotating m/z features against a metabolite database

Use when parsing, standardizing, or filtering MS spectra from mixed or

Use when you have a set of in silico-predicted compounds (with SMILES

Use when when you have a list of target molecules with known molecular

Use when when you have a metabolite SMILES structure and need to predict

Use when you have computed a histogram of pairwise mass differences from

Use when you have computed a histogram of mass differences from all pairwise

Use when after identifying statistically significant LC-MS features (e.g.

Use when when you have an LC-MS feature table with m/z and retention

Use when when processing LC-MS metabolomics feature tables where adduct

Use when when you have a list of observed m/z values from LC/MS feature

Use when ingesting mass spectrometry spectra from heterogeneous databases

Use when you have statistically significant LC-MS features (e.g., filtered

Use when when you have access to annotated MS/MS spectra from a specific

Use when you have an unknown MS/MS spectrum with a measured precursor

'Use when you have a validated or curated dataset (e.g., a TSV or gzip-compressed

Use when you have a feature table from untargeted LC–MS all-ion fragmentation

Use when you have vendor mass spectrometry raw files (e.g., .raw, .d,

Use when you have multiple independent peak-picking algorithms available

Use when when you need to evaluate how a specific algorithm parameter

Use when you have refactored or reimplemented a core computational method

Use when when you have extracted feature tables from multiple breath

Use when after multi-sample alignment has been completed in JPA (Part

Use when after retention time and m/z-based clustering have been applied

Use when you have predicted peptide sequences from a de novo sequencing

Use when after MS2Query has ranked and scored library matches against

'Use when preparing to run LipidMatch-4.2 and you need to determine which

Use when you have measured metabolites or lipids from biobanked or processed

Use when you have raw chromatography–mass spectrometry data (GC-MS or

Use when after applying a stringent Q-value quality filter (e.

Use when you are evaluating a new or existing data analysis pipeline