Coding & Dev Tools

holobiomicslab Skill

Use when you need to confirm that omitting an optional input parameter (such as secondaryAssay in buildExperiment) produces the expected mathematical result—specifically, when a default value should neutralize a transformation (e.

holobiomicslab Skill

Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z values to a reference database and want to recover HMDB identifiers, molecular formulas, and structural annotations for.

holobiomicslab Skill

Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.

holobiomicslab Skill

Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw chromatogram.

holobiomicslab Skill

Use when when you have raw untargeted LC/MS data in mzML or mzXML format and need to detect and quantify metabolite signals across mass-to-charge and retention time dimensions without prior knowledge of instrument parameters, batch effects, or optimal detection thresholds.

holobiomicslab Skill

Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.

holobiomicslab Skill

Use when you need to generate a set of candidate chemical formulas for LC-MS/MS simulation—specifically when you want to populate a virtual mass spectrometer with realistic chemical structures drawn from a reference database (HMDB) or a uniform m/z distribution, and you need to apply m/z filtering.

holobiomicslab Skill

Use when you have two separate LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to establish feature-to-feature correspondence between them.

holobiomicslab Skill

Use when after retrieving top-scoring library candidates from a full MS2Deepscore comparison, but before or during final re-ranking.

holobiomicslab Skill

Use when when you have a query MS/MS spectrum (m/z and intensity pairs) and need to find potential structural analogues or exact matches in a large spectral library. Apply this skill after preprocessing your spectra (e.

holobiomicslab Skill

Use when you have an aligned feature table from untargeted LC-MS with missing intensity values (NA or zero entries) for features that are present in some samples but fell below detection threshold in others.

holobiomicslab Skill

Use when after completing peak picking, sample alignment, and before final MS2 spectrum extraction, when you have identified individual ion peaks across samples and need to link isotopic variants (e.

holobiomicslab Skill

Use when you have a preprocessed peak table from tandem MS/MS data (e.

holobiomicslab Skill

Use when after creating a GNPS mass spectral molecular network and running an MS2LDA experiment, use this skill when you want to identify and visualize which substructural motifs (Mass2Motifs) are shared across clustered spectra, particularly to highlight fragmentation pattern similarities between.

holobiomicslab Skill

Use when a user submits one or more MS/MS spectra (via .mgf file, USI list, or direct upload) and the downstream analysis requires dispatching to a specific domain-specific MASST tool (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST, or metadataMASST).

holobiomicslab Skill

Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.

holobiomicslab Skill

Use when when aggregating MS/MS spectra from multiple public repositories (GNPS, MassBank, Mona) or in-house sources with inconsistent metadata naming conventions, missing or malformed adduct annotations, or incomplete chemical structure annotations (SMILES/InChI/InChIKey).

holobiomicslab Skill

Use when you have preprocessed MS/MS spectra (noise-filtered, normalized) and need to compute pairwise similarity or distance scores for compound library matching, when your goal is to rank candidate compounds by spectral match quality and maximize correct identification rate above dot-product.

holobiomicslab Skill

Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental metadata from tabular spreadsheets, you need to map certain fields to computed or filtered values, apply conditional.

holobiomicslab Skill

Use when when preparing a software release, testing contribution workflows, or auditing package availability: verify that matchms can be installed and imported successfully from all advertised distribution channels (PyPI and Bioconda) to confirm the package metadata, dependencies, and entry points.

holobiomicslab Skill

Use when when uploading or ingesting paired omics project documents into the Pairing Omics Data Platform, or when you need to verify that a JSON project file conforms to the expected schema structure before processing MS/MS mass spectra linkages, genome associations, or submission to external.

holobiomicslab Skill

Use when after completing an Environment simulation run with save_eval flag enabled, when you need to preserve the EvaluationData object containing scan provenance, chemical source definitions, and fragmentation events for later inspection, validation, or reanalysis without re-running the full.

holobiomicslab Skill

Use when you have computed empirical p-values from randomized sampling (e.

holobiomicslab Skill

Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.

holobiomicslab Skill

Use when when you have loaded search result files from one or more DIA-MS analysis tools and need to assess the quantitative performance of identified features.

holobiomicslab Skill

Use when when you have a quantitative feature table from MZmine2/MZmine3 with peak area and m/z data aligned across multiple extract samples, and you need to identify which features are characteristic of individual samples (high specificity) versus ubiquitous across the extract set.

holobiomicslab Skill

Use when when you have GC-MS data with detected peaks that require structural annotation, retention index calibration has been applied (typically using FAMES standards), and you need to assign compound identities with confidence scores.

holobiomicslab Skill

Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against reference libraries such as PNNLMetV20191015.MSL.

holobiomicslab Skill

Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all-pairs or many-to-many spectrum similarity to identify related compounds, build spectral libraries, or perform large-scale library searching.

holobiomicslab Skill

Use when after XCMS peak picking, alignment, and grouping when you have identified putative incorporations (via PuInc_seeker) or base-peak isotopologue candidates and need to exclude low-intensity peaks that are likely noise or instrument artifacts.

holobiomicslab Skill

Use when when XCMS-aligned LC-MS data shows coefficient of variation (CV) above expected thresholds for known features, or when analyzing long-duration experiments (>1 week) or large cohorts (>100 samples) where global warping functions are known to fail due to compound-specific RT drift structures.

holobiomicslab Skill

Use when you have centroided MS2 spectra (in mzML format from data-dependent acquisition) and a list of known or suspect PFAS diagnostic fragment masses, and you need to systematically flag which detected features contain fragments characteristic of PFAS compounds (e.

holobiomicslab Skill

Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract the predicted molecular fingerprint representation and associated scoring metrics for compound identification or CANOPUS.

holobiomicslab Skill

Use when when performing targeted peak detection on LC-MS data where compounds have been assigned expected ionization polarities (positive or negative mode) in the target list, and you want to prevent false peak assignments from the opposite polarity and avoid manual pre-filtering of raw data by.

holobiomicslab Skill

Use when you have loaded raw tandem MS spectra (in MGF, mzML, or similar format) and need to prepare them for peptide identification, spectral library matching, or intensity-based analysis.

holobiomicslab Skill

Use when when preparing augmented training data for Siamese or contrastive learning architectures in mass spectrometry, specifically when you need to generate hard negative examples that are spectrally distinct but mass-similar to positive examples.