Coding & Dev Tools

holobiomicslab Skill

Use when when you have raw TWIM-MS arrival-time data and need to transform it into absolute CCS values for downstream biomolecular class assignment or comparative analysis.

holobiomicslab Skill

Use when when you have multi-omic TWIM-MS data (raw or processed arrival-time records) and have already assigned features or detected ion features to biomolecular classes (e.

holobiomicslab Skill

Use when you have raw mass spectra data (MGF format with m/z/intensity pairs) that need to be clustered rapidly, especially on large-scale proteomics datasets (millions of spectra).

holobiomicslab Skill

Use when you have retrieved a user database entry (sequence or building-block structure record) from the MassSpecBlocks backend and need to generate a file in CycloBranch format for mass spectra analysis, interpretation, or sharing with collaborators using the CycloBranch software.

holobiomicslab Skill

Use when you need to export a stored chemical structure (sequence or building-block entry) from the MassSpecBlocks database to enable mass spectra analysis in CycloBranch or when preparing structures for import into other cheminformatics workflows that require a standardized structure interchange.

holobiomicslab Skill

Use when you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to assess which library compounds are structurally similar to your queries, retrieve their categorical annotations (e.

holobiomicslab Skill

Use when when you have a normalized metabolite abundance matrix with sample metadata assigning each sample to one of three or more distinct biological classes (e.

holobiomicslab Skill

Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.

holobiomicslab Skill

Use when when processing raw untargeted LC/MS data in mzML or mzXML format and you need to detect peaks across mass-to-charge (m/z) and retention time (rt) dimensions without prior knowledge of optimal signal detection parameters, QC samples, or domain expertise in LC/MS preprocessing.

holobiomicslab Skill

Use when you have acquired MS/MS spectra containing suspect noise ions—either electronic noise (ions with identical intensities occurring >4 times in a single peak list, a signature of detector artifacts) or chemical noise (fragment ions chemically implausible given the precursor molecule's.

holobiomicslab Skill

Use when you have a QC-annotated feature table (samples × features with QC sample identifiers) from LC-MS untargeted metabolomic profiling and observe systematic signal drift across the run sequence or between batch blocks.

holobiomicslab Skill

Use when when applying a series of mpactr filter functions (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) with copy_object=FALSE to confirm that the original peak table object is mutated as intended, not silently copied.

holobiomicslab Skill

Use when when you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.

holobiomicslab Skill

Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures or defer initialization until data access.

holobiomicslab Skill

Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient separation between validated links and the background population.

holobiomicslab Skill

Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction spline.

holobiomicslab Skill

Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit overlapping spatial distributions across the tissue image that could confound downstream annotation filtering.

holobiomicslab Skill

Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries from a MotifDB reference database.

holobiomicslab Skill

Use when you have 2D NMR spectral data (heteronuclear and/or homonuclear experiments) from multiple samples in a natural products library or mixture, and you need to identify common structural scaffolds, correlate features across samples, or prioritize samples for further structural annotation.

holobiomicslab Skill

Use when traditional peak extraction algorithms have produced a feature table that you suspect is incomplete or missing known suspects from your target database (e.g., T3DB).

holobiomicslab Skill

Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.

holobiomicslab Skill

Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it.

holobiomicslab Skill

Use when after chromatographic peak detection (findChromPeaks) when you have a processed XcmsExperiment object with detected peaks and need to perform initial feature grouping. Use it when features of the same compound are expected to co-elute within a narrow retention-time window (e.

holobiomicslab Skill

Use when after generating aligned MS2 fingerprints (sample-by-fingerprint matrices) from metabolomics data when you need to visually inspect sample clustering, identify sample similarities, or detect batch effects and RT shifts across different LC methods or mass spectrometer technologies.

holobiomicslab Skill

Use when after performing spectral library matching of mass spectrometry peaks against a fragmentation library (e.

holobiomicslab Skill

Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically when clustering bottom-up proteomics data with the goal of grouping spectra from the same peptide sequence or when you.

holobiomicslab Skill

Use when you have a noisy MS/MS spectrum and need to identify and remove chemical noise ions (as opposed to electronic noise). You have the precursor compound's SMILES string or molecular formula and its adduct type.

holobiomicslab Skill

Use when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to identify and quantify metabolic features before multi-sample alignment. Use MS1 peak picking for full-scan or DDA data to extract Gaussian and non-Gaussian shaped peaks;

holobiomicslab Skill

Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for a known metabolite.

holobiomicslab Skill

Use when you have mass spectrometry spectra stored across multiple, disparate metabolomics repositories (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA) and need to retrieve them using a single identifier scheme, or you are publishing spectrum figures and need.

holobiomicslab Skill

Use when rescoring PSMs with machine learning or statistical models where: (1) you want to consider multiple candidate PSMs per spectrum (e.

holobiomicslab Skill

Use when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to inspect peak structure, verify instrument performance, or generate baseline visualizations before downstream peak annotation or statistical analysis.

holobiomicslab Skill

Use when you have measured MS intensity data from unknown samples and known-concentration standard compounds, and you need to convert sample intensities into predicted concentrations. Specifically applicable when intensity drift is observed across the measurement sequence (e.

holobiomicslab Skill

Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which ones are explicitly stored in your backend.

holobiomicslab Skill

Use when after the Proteomics_Data_Processor tool has completed analysis of raw mass spectrometry files and returned structured output records.

holobiomicslab Skill

Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).