Coding & Dev Tools

holobiomicslab Skill

Use when after molecular formula assignment from FT-ICR MS peak data, when you need to classify metabolites by their redox state to predict bioavailability or lability, or when generating thermodynamic indices for chemodiversity analysis and environmental metabolomic interpretation.

holobiomicslab Skill

Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.

holobiomicslab Skill

Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting without access to spectral libraries.

holobiomicslab Skill

Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for metabolite annotation, and the matrix is not yet configured in your Met-ID installation.

holobiomicslab Skill

Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time dimensions. Use this skill when you must isolate individual ion signals before applying calibration corrections (e.

holobiomicslab Skill

Use when you have LC-MS/MS data in mgf format and a custom spectral database prepared with CFM-id (or an in-built database), and you need to identify unknown compounds by comparing their experimental fragmentation patterns against predicted or reference spectra with quantified match scores.

holobiomicslab Skill

Use when you need to create a synthetic feature table with known, ground-truth condition effects for method validation when: (1) testing normalization or batch-correction algorithms that must not confound condition signal with batch noise;

holobiomicslab Skill

Use when after initial retention-time-based feature grouping when you have groups of multiple features at similar m/z and retention time but need to determine which features actually arise from the same compound.

holobiomicslab Skill

Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) and need to establish reliable correspondence between features across datasets.

holobiomicslab Skill

Use when when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict its tandem mass spectrum for structural elucidation or mass spectrometry validation.

holobiomicslab Skill

Use when you have candidate metabolite structures (from database lookup or enumeration) and experimental MS/MS spectra (mzML, mzXML format), and need to rank candidates by how well their predicted fragments match observed peaks.

holobiomicslab Skill

Use when you have clustered peak networks from INADEQUATE NMR spectra (output from the Clustering module) and need to assign metabolite identities by comparing them to known spectral signatures.

holobiomicslab Skill

Use when you have raw LC-IMS-MS data (Agilent, Thermo, Bruker, or mzML format) and need to visualize and export the spatial distribution of a specific ion species (or ion family) across both ion mobility and retention time dimensions.

holobiomicslab Skill

Use when you have an XCMS-processed feature set (XCMSet object) from replicate LC/MS runs comparing labeled (e.g., 13C-glucose) and unlabeled (e.g., 12C-glucose) conditions, and need to identify which features show isotope incorporation (fold-change ≥1.5, p-value <0.

holobiomicslab Skill

Use when after MS-DIAL peak character estimation has grouped LC-MS features into preliminary clusters based on peak shape and chromatographic similarity, and you need to select a single representative parental feature from each cluster to reduce redundancy before MS-FINDER annotation.

holobiomicslab Skill

Use when after Mass2Motifs have been inferred from tandem MS/MS spectra via LDA topic modeling and you need to assign putative substructure annotations to those motifs.

holobiomicslab Skill

Use when you have a user-submitted spectrum with domain-context metadata (e.

holobiomicslab Skill

Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to consolidate redundant or related ion signals into compound-level feature groups before downstream statistical or.

holobiomicslab Skill

Use when after features have been identified in LC-MS data via peak picking, MS2 recognition, or targeted-list matching, and you need to measure their signal magnitude (peak height or area) across samples for quantitative comparison, normalization, or statistical testing in metabolomics studies.

holobiomicslab Skill

Use when when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to track which version of the table is being used at each step.

holobiomicslab Skill

Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.

holobiomicslab Skill

Use when when preparing tandem MS/MS data for spectral alignment and similarity comparison, particularly when you have loaded raw fragmentation spectra and need to extract and quantify mass difference patterns that capture the fragmentation process.

holobiomicslab Skill

Use when you have an tandem MS spectrum with unidentified peaks and a known or hypothesized peptide sequence (in ProForma 2.0 format, including post-translational modifications).

holobiomicslab Skill

Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using hierarchical clustering.

holobiomicslab Skill

Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a reference using 2D correlation optimized warping) and need to consolidate them into a single analytical object for.

holobiomicslab Skill

Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to an mpactr object and generating a qc_summary() data.

holobiomicslab Skill

Use when after calling MsmsSpectrum.annotate_proforma() to assign fragment ions to a mass spectrum, verify that each annotated peak has the correct ion_type ('b' or 'y'), charge state, and m/z deviation from the theoretical mass computed for that peptidoform.

holobiomicslab Skill

Use when you have raw LC-MS metabolomics data from multiple disease groups (in .npy or .

holobiomicslab Skill

Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb, joblauncher, job, pubchem) receives the correct configuration—such as port mappings, service URLs, and data paths—without.

holobiomicslab Skill

Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.

holobiomicslab Skill

Use when after executing MassQL queries on mass spectrometry data that produce tabulated results (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to persist those results for archival, sharing, or downstream statistical analysis.

holobiomicslab Skill

Use when you have loaded an FT-ICR raw spectrum (e.g., ESI_NEG_SRFA.d in Bruker or ThermoFisher .raw format) and need to identify the m/z positions and intensities of individual mass spectral peaks.

holobiomicslab Skill

Use when when you need to create synthetic noisy MS/MS spectra from clean baseline spectra to validate denoising algorithms, compare denoising performance across noise levels, or generate ground-truth test datasets where the true signal and noise composition are known and controllable.

holobiomicslab Skill

Use when after applying batch correction (e.g., via pycombat) to a multi-batch feature table, to validate whether the correction has reduced systematic intensity differences between batches.

holobiomicslab Skill

Use when after running a scoring algorithm (e.g., MetcalfScoring) on paired genomic and metabolomic datasets.

holobiomicslab Skill

Use when when you have a peaklist from IDSL.IPA or similar peak-picking tools (containing observed m/z and intensity values) and need to assign molecular formulas from a prioritized chemical space.