Claude Skills by HolobiomicsLab

Use when after chromatographic peak detection on preprocessed LC-MS data

Use when when processing Data Dependent Acquisition (DDA) raw mass spectrometry

Use when you have LC-MS data from authentic standards run in positive

'Use when after mass track construction and before composite map building,

Use when after mass track extraction and alignment across samples, when

Use when you have extracted feature tables (via MS1 peak picking, MS2

Use when you have an XCMS CentWave feature extraction output table containing

Use when after matching mass-to-charge ratios to a compound database

Use when you have multiple LC-MS runs with the same set of targets (compounds)

Use when you have detected multiple LC-MS features (m/z peaks) across

Use when when you have detected multiple features from non-targeted mass

Use when after componentization of parent and TP features with generateComponents(algorithm='tp'),

Use when you have LC-MS data processed through XCMS grouping that shows

'Use when you have multidimensional MS data converted to MZA HDF5 format

Use when when you have Thermo Orbitrap .raw files containing known reference

Use when after chromatographic peak detection (findChromPeaks) when you

Use when you have extracted retention times from top MS1 features in

Use when working with GCIMS datasets where retention time spans a wide

Use when you have acquired a bottom-up proteomics LC-MS/MS run (e.

Use when you have Thermo Fisher Scientific .raw files from an LC-MS experiment

Use when you have xcms-processed LC-MS data with detected misaligned

Use when when you have imported mass spectrometry data in .raw, .d, or

Use when when you have a resolved mzML or mzXML spectrum file and need

Use when after anchor feature pairs (m/z and retention time values) have

Use when you have two independent LC-MS untargeted metabolomic feature

Use when you have two LC-MS untargeted metabolomic feature tables (each

Use when after sample alignment and grouping of isotopologues and adducts

Use when you have multiple feature tables (CSV files) from different

Use when you have extracted feature tables (m/z, intensity, retention

Use when processing raw LC/MS data (mzML or mzXML format) from multi-sample

Use when when you have mass-spectrometry data in tabular form (Pandas

Use when you have LC-HRMS profile-mode data (e.g., netCDF or mzML format)

Use when when you have parsed .mzML or Thermo .raw LC-MS data and need

Use when you have processed LC-MS run data (feature table or peak detection

Use when you have XCMS-aligned feature tables with retention time values

Use when after applying peak detection algorithms to identify local maxima

Use when after drift correction and quality flagging, when you have a

Use when you have a new chromatographic dataset with molecular structures

Use when you have molecular structures (SMILES or SDF format) for which

Use when you have a set of small-molecule compounds (e.g., from MS/MS

Use when when you have a retention-time dataset (e.g., SMRT or Eawag_XBridgeC18_364)

Use when you have a list of candidate metabolites for an unknown compound

Use when after training a GNN-RT model on preprocessed molecular graph

Use when you have MS1-formatted mass spectrometry files from a liquid

Use when when you have retention times measured on one chromatographic

Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format)

Use when after initializing and executing a forward pass through a dual-branch

Use when when you have loaded an LC-MS spectrum file (mzML, mzXML, or

Use when after filtering LC-MS features by statistical significance (e.g.,

Use when you have loaded sqMass files containing pre-extracted transition