Coding & Dev Tools

holobiomicslab Skill

Use when you have a set of in silico-predicted compounds (with SMILES structures) and an experimental metabolomics peak list (m/z values), and you need to filter predictions to only those that could plausibly be detected.

holobiomicslab Skill

Use when when implementing a custom MsBackend subclass and need to verify that spectra variables (e.g., precursor m/z, retention time, MS level) conform to expected data types before exposing them to Spectra objects.

holobiomicslab Skill

Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across the ion mobility axis.

holobiomicslab Skill

Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic coverage) in its README, and you need to create a machine-readable inventory for downstream indexing, validation, or reuse.

holobiomicslab Skill

Use when when benchmarking or validating a pathway analysis method (such as PALS, ORA, or GSEA) on metabolomics data, you need quantitative evidence that the method's pathway rankings remain stable despite noise and missing peaks—conditions prevalent in real LC-MS/MS datasets.

holobiomicslab Skill

Use when when you have raw feature tables exported from a tandem LC-MS/MS preprocessing tool (e.g., Progenesis QI, MS-DIAL, Bruker Metaboscape) and need to combine them with sample metadata (group assignments, replicate structure) before applying feature filtering or quality control workflows.

holobiomicslab Skill

Use when you have acquired MS-DIAL peak lists in both positive and negative ionization modes on the same sample set and want to consolidate detected features across modes to avoid reporting duplicate annotations for the same molecule.

holobiomicslab Skill

Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate LC-MS retention time linearity, assess method reproducibility, or establish retention time calibration curves.

holobiomicslab Skill

Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z and intensity; columns = samples) and need to assign KEGG compound identifiers to observed peaks.

holobiomicslab Skill

Use when after MamsiStructSearch has completed structural clustering of statistically significant LC-MS features (p < 0.

holobiomicslab Skill

Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to features falling below the detection limit in some samples but being present above-threshold in others.

holobiomicslab Skill

Use when you have embedded sequences of chemical formulae (tokenized and converted to dense vectors) from tandem MS/MS spectra and need to learn context-dependent representations that capture dependencies between formula tokens at multiple semantic levels.

holobiomicslab Skill

Use when after temporal correlation has identified candidate feature pairs with matching intensity profiles across time-resolved DBDI-MS experiments.

holobiomicslab Skill

Use when when you have binned mass spectrometry imaging peaks and want to understand which detected mass-to-charge ratios represent the same metabolite in different ionization states (parent vs. adduct form).

holobiomicslab Skill

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

holobiomicslab Skill

Use when when you have a molecular geometry (XYZ format) and need to predict electron ionization (EI) mass spectrum fragmentation patterns by exhaustively sampling conformational space and reaction intermediates.

holobiomicslab Skill

Use when you have executed multiple NPDtools database search pipelines (Dereplicator, VarQuest, Dereplicator+, or MetaMiner in different modes) on identical test spectra or RiPP sequence inputs and need to understand their relative sensitivity, specificity, and complementarity.

holobiomicslab Skill

Use when when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to extract metabolic features as the first major step of untargeted metabolomics analysis. Choose MS1 peak picking for DDA/full-scan data;

holobiomicslab Skill

Use when after chromatographic peak detection on preprocessed LC-MS data, when you have hundreds or thousands of individual m/z × retention-time peaks and need to associate them into biologically meaningful feature groups.

holobiomicslab Skill

Use when when importing candidate metabolite structures from public chemical databases (PubChem, ChEBI, etc.) for use in MAGMa-based annotation workflows, or when integrating external structure datasets that may use divergent molecular representation formats or contain non-standard chemical.

holobiomicslab Skill

Use when you have molecular identifiers (SMILES strings or molecular structure files) that need to be converted into node-edge graph tensors for input to message passing neural network models like chemprop or chemprop-IR.

holobiomicslab Skill

Use when you have a GNPS mass spectral molecular network (in .graphml or Cytoscape format) and wish to annotate its nodes and edges with chemical class assignments from the GNPS library and/or MS2LDA motif probabilities from an independent LDA experiment.

holobiomicslab Skill

Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine whether they capture complementary information that justifies combining them.

holobiomicslab Skill

Use when after running annotateRC() on LC-MS AIF features, when you need to validate whether a feature's rank-1 annotation is reliable or when you suspect that structurally similar metabolites (e.

holobiomicslab Skill

Use when you have executed batch searches across two or more domain-specific MASST tools and obtained separate output files (_microbe.json, _plant.json, _tissue.

holobiomicslab Skill

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

holobiomicslab Skill

Use when when you have antiSMASH-predicted BGCs and wish to link them to metabolomic data via structure prediction, but only BGCs with sufficient structural homology to characterized reference clusters will yield reliable predictions.

holobiomicslab Skill

Use when after structural clustering (isotopologue grouping, adduct detection, cross-assay linking) and correlation clustering of LC-MS features, when you need to inspect and communicate the topology of structural relationships—particularly when the number of features or link types is too dense for.

holobiomicslab Skill

Use when after isotope detection has enumerated C13 isotopologue patterns across m/z, drift time, and retention time dimensions, and you need to reduce false positives by retaining only well-populated isotopic signature clusters before annotation or export.

holobiomicslab Skill

Use when you have two independent LC-MS untargeted metabolomic feature tables (e.

holobiomicslab Skill

Use when you have detected peaks from untargeted LC/HRMS analysis (via IDSL.IPA or equivalent peak picker) with m/z and retention time values, and you need to assign molecular formulas to those peaks.

holobiomicslab Skill

Use when after LDA has converged and inferred Mass2Motifs from preprocessed mass spectrometry spectral data, when the raw motif-fragment distributions contain noise or low-confidence associations that obscure the dominant fragmentation patterns.

holobiomicslab Skill

Use when you have a Thermo Fisher Orbitrap .raw file and need to retrieve a specific scan's spectral data (m/z and intensity arrays), validate instrument parameters (resolving power, AGC injection time), or assess signal-to-noise characteristics of fragment ions for a known precursor peptide (e.

holobiomicslab Skill

Use when a Shiny application or R-based tool is known to run on only one operating system (e.g., Windows-only), and you need to identify the root causes preventing execution on Linux or macOS before undertaking cross-platform porting.

holobiomicslab Skill

Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.

holobiomicslab Skill

Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts between acquisitions, or use of different LC-MS platforms (e.g., Orbitrap vs. Q-ToF).