Coding & Dev Tools

holobiomicslab Skill

Use when after chromatographic peak detection on preprocessed LC-MS data, when you have detected features (peaks) in multiple samples and need to establish which peaks across samples represent the same molecular species.

holobiomicslab Skill

Use when you have a feature table from LC- or GC-HRMS data (either detected via pyOpenMS or imported as a custom feature list) containing m/z, retention time, and intensity values, and you want to rapidly filter to candidate PFAS features that exhibit the elevated mass defects typical of.

holobiomicslab Skill

Use when after retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra. Use this skill to confirm the network structure is sound before performing chemical similarity searches, community detection, or annotation.

holobiomicslab Skill

Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context for downstream biosynthetic gene cluster or chemical ecology analysis.

holobiomicslab Skill

Use when you have detected features in LC- or GC-HRMS data (via pyOpenMS or custom feature tables) and need to systematically rank them for likelihood of being PFAS compounds.

holobiomicslab Skill

Use when when working with large metabolomics peak tables (e.

holobiomicslab Skill

Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation pattern against a pre-indexed spectral library using learned spectral embeddings.

holobiomicslab Skill

Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters. Use this skill when: (1) you have a sparse similarity or distance matrix as input;

holobiomicslab Skill

Use when you have a GC-MS results table with a Match.Factor column (representing identification confidence) and you need to understand how many distinct compounds survive at different quality cutoffs (e.g., ≥65, ≥80, ≥90).

holobiomicslab Skill

Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign unidentified features to biomolecular classes (e.

holobiomicslab Skill

Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability across languages and tools; (2) load mzPeak spectrum or chromatogram data into memory as structured tables for analysis;

holobiomicslab Skill

Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full pathway database should serve as the statistical background, and which pathways contain how many metabolites overall.

holobiomicslab Skill

Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to confirm that the resulting arrays fall within specified m/z windows, intensity bounds, and peak count limits before.

holobiomicslab Skill

Use when after sample alignment and isotopologue/adduct grouping are complete, when you need to associate MS2 spectral data (DDA-acquired) with the consolidated feature groups to enable MS/MS-based compound annotation or to bundle MS1 quantification with MS2 evidence.

holobiomicslab Skill

Use when after peak detection on a composite mass track has identified candidate peaks in a mass chromatogram, and before compiling the final feature table.

holobiomicslab Skill

Use when you have a MemoMatrix (sample-by-fingerprint matrix) from aligned MS2 spectra and need to visually compare sample similarity or clustering patterns, especially when samples show poor feature overlap, strong retention time shifts across different LC methods, or were acquired on different.

holobiomicslab Skill

Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate annotations per feature, visualize matched ions in ranked spectra, or export pseudo-MS/MS spectra for external analysis.

holobiomicslab Skill

Use when you have a large indexed gzip file (igz format) with metadata encoded in the gzip header comment field, and you need to retrieve specific blocks or spectra by integer index without decompressing the entire file.

holobiomicslab Skill

Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on declared input type (LC, GC, IMS, or MS Imaging).

holobiomicslab Skill

Use when you have computed high-dimensional embeddings (e.

holobiomicslab Skill

Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic detection, or wishes to augment/replace pyOpenMS results with pre-processed features.

holobiomicslab Skill

Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment libraries (e.g., LipidPos for lipids).

holobiomicslab Skill

Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).

holobiomicslab Skill

Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest neighbors efficiently.

holobiomicslab Skill

Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the scheduled method with correct temporal spacing.

holobiomicslab Skill

Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a compound-class-agnostic method.

holobiomicslab Skill

Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may represent the same compound ionized as different adducts (e.g., [M+H]⁺ vs. [M+Na]⁺).

holobiomicslab Skill

Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool. The skill is required whenever you are preparing MS-DIAL output for consumption by external analysis pipelines that expect standardized export formats.

holobiomicslab Skill

Use when when you have LC-MS normalized intracellular metabolite abundance measurements for multiple cell lines and need to estimate reaction activity driven by substrate availability rather than enzyme expression alone.

holobiomicslab Skill

Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by precursor m/z).

holobiomicslab Skill

Use when when calling filter functions (e.g., filter_mispicked_ions(), filter_group(), filter_cv()) on R6-based metabolomics data objects in the mpactr package and you need to verify whether the original object's state is preserved.

holobiomicslab Skill

Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.

holobiomicslab Skill

Use when you need to validate the reference-semantics behavior of mpactr filter functions, particularly when using copy_object=FALSE. Use it to confirm that a filtering operation (e.

holobiomicslab Skill

Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.

holobiomicslab Skill

Use when when contributing code changes to a Python project (fork, feature branch, or pull request) that uses a setup.py-based test suite, before pushing changes to the remote repository or merging into the main branch.

holobiomicslab Skill

Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral analysis.