Integrations & APIs

holobiomicslab Skill

Use when when you have separate quantification data (abundance matrix), sample metadata (phenotypes, treatment groups, experimental conditions), and spectral data (MS/MS fragmentation patterns or other spectral features) that must be combined for mass spectrometry-based metabolite analysis.

holobiomicslab Skill

Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to assign biomolecular class labels and compute class-specific CCS values across multiple compound classes simultaneously, particularly when you lack pre-identified feature peaks or want to bypass.

holobiomicslab Skill

Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.

holobiomicslab Skill

Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.

holobiomicslab Skill

Use when you have raw mass spectrometry data in mzML or mzXML format and need to compress it using a format-agnostic compressor that expects a standardized spectral data contract.

holobiomicslab Skill

Use when you have NMR peak data (1H and 13C chemical shift values) that must be submitted to a remote DeepSAT SMART 3 classification API for structural prediction, and you need to format the data correctly, validate the endpoint schema, and parse the response to extract predictions and confidence.

holobiomicslab Skill

Use when when a QC check fails during an active LC-MS run and configured email notification targets exist in the system. Use this skill to ensure that QC failures are communicated to stakeholders immediately, complementing Slack-based alerts for users who prefer or require email notification.

holobiomicslab Skill

Use when when you have Thermo Fisher RAW mass spectrometry files and need to extract mass-to-charge ratios, intensities, scan metadata, and peak lists within a Python script or notebook for downstream computational analysis, and you require programmatic control over extraction parameters rather.

holobiomicslab Skill

Use when when you have multiple mass spectrometry data formats (mzML, mzXML, or others) that must be ingested into a single format-agnostic processing engine (e.g., mspack compression), and you need to avoid replicating the core logic for each format.

holobiomicslab Skill

Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared structural features or chemical families across spectral clusters.

holobiomicslab Skill

Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.

holobiomicslab Skill

Use when you have MS data in a new format or storage system (e.g., a custom database, HDF5 file, or proprietary raw file) and need to make it accessible to Spectra-based analysis workflows without forking the Spectra package itself.

holobiomicslab Skill

Use when you have a Universal Spectrum Identifier (USI) string referencing a spectrum in a supported metabolomics repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, MassIVE, or MS2LDA) and need to create an embeddable, scannable reference for publication or data integration that.

holobiomicslab Skill

Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to populate them by querying multiple independent web APIs in parallel.

holobiomicslab Skill

Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar TensorFlow Serving-backed molecular classification system that expects peaks as JSON rather than raw spectroscopic files.

holobiomicslab Skill

Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did not yield detected peaks at certain cluster positions.

holobiomicslab Skill

Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have a feature table with identified ISF features and their hierarchical fragmentation relationships, and you need to export this relationship structure for interpretation, integration with external.

holobiomicslab Skill

Use when when you have implemented or modified a data ingestion module (e.g., mzML parser) and need to verify that file deserialization produces correct internal representations.

holobiomicslab Skill

Use when when you have downloaded a GNPS molecular networking archive (GNPS1 or GNPS2 workflow output) and need to reconstruct spectral records for integration with genomic data (BGCs, antiSMASH results) or for computing molecular family links and spectral similarity scores.

holobiomicslab Skill

Use when when you have a multi-step computational workflow (e.g., peak detection, filtering, manual review) implemented in R and need to expose it to end-users who lack R expertise.

holobiomicslab Skill

Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public repository, and you need to apply that method to new experimental data (e.

holobiomicslab Skill

Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular fingerprint predictions, de-novo candidate structures, or chemical class annotations without maintaining local neural network.

holobiomicslab Skill

Use when when a backend service receives structured prediction results from an external API (e.g., nmrshiftdb peak predictions) and must return them to a client application via HTTP POST response.

holobiomicslab Skill

Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API. The peaks must be reformatted from their native instrument output into JSON before submission to the /api/smart3/search endpoint.

holobiomicslab Skill

Use when you need to verify that a Python package (or similar installable software) passes its declared integration test suite as a prerequisite to trusting its reliability in production or downstream analysis. Specifically, apply it when you observe a periodic testing CI workflow badge (e.

holobiomicslab Skill

Use when you have DIA mass spectrometry raw files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) in their native formats (.raw, .d, .

holobiomicslab Skill

Use when you have search result files from one or more DIA-MS analysis tools and need to load them into a unified environment for Q-value filtering, cross-tool comparison (upset plots), and interactive visualization of identifications, quantifications, and coefficient of variation metrics across.

holobiomicslab Skill

Use when you have structural candidates from in silico tools (SIRIUS/CANOPUS) and library spectral matches from GNPS, but need to resolve conflicting or incomplete chemical classifications into a unified consensus.

holobiomicslab Skill

Use when when you need to validate that a package's periodic integration test suite (distinct from unit tests) passes as expected, or when you must collect and communicate structured evidence of test outcomes across multiple test cases.

holobiomicslab Skill

Use when you have centroid-mode LC–MS all-ion fragmentation (AIF) data already processed through xcms for feature detection and retention-time correction, and a corresponding RamClustR object that groups co-eluting fragment ions into putative spectral clusters.

holobiomicslab Skill

Use when you need to construct a reference metabolomics database from scratch or when existing public databases (HMDB, MassBank, METLIN) need to be merged into a single queryable resource for metabolite annotation in untargeted mass spectrometry analysis.

holobiomicslab Skill

Use when you have computed frequent fragmentation patterns from a collection of MS/MS spectra using mineMS2, and you want to focus pattern interpretation on subsets of spectra that form meaningful network components (connected groups, cliques, or high-similarity pairs) in a GNPS molecular network.

holobiomicslab Skill

Use when when you have (1) a molecular network graph from GNPS with node identifiers and edges, (2) LC-MS/MS features quantified across fractions in a feature table, and (3) bioassay measurements (e.

holobiomicslab Skill

Use when after cluster-based filtering has produced a set of candidate KEGG compounds for each feature cluster in untargeted LC-MS data, and you need to rank these candidates by their metabolic plausibility using network context rather than mass accuracy alone.

holobiomicslab Skill

Use when when you have deposited a collection of JSON project documents in a platform or repository and need to verify that all conform to a published JSON Schema specification before publication, distribution, or integration with downstream systems.

holobiomicslab Skill

Use when when you have converted multidimensional MS data to MZA HDF5 format and need to programmatically read spectra, metadata, and ion mobility or mass-to-charge arrays in Python or R without vendor-specific dependencies.