Coding & Dev Tools

holobiomicslab Skill

Use when you have a merged MGF file (e.g., from MZmine output) containing MS/MS spectra from multiple biological or environmental samples, and you need to process each sample independently through annotation pipelines (e.

holobiomicslab Skill

Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among thousands of detected features.

holobiomicslab Skill

Use when after applying a filter function (filter_mispicked_ions(), filter_group(), filter_cv(), filter_insource_ions()) to an mpactr object, use this skill to inspect and document which features were retained versus removed.

holobiomicslab Skill

Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be resolved by simple peak picking.

holobiomicslab Skill

Use when when setting up matchms for the first time in a new environment, after upgrading Python or conda, when switching between package managers (pip vs conda), or when distributing matchms to end users to confirm functionality across supported installation channels.

holobiomicslab Skill

Use when you have two MemoMatrix objects generated from separate sample cohorts (e.

holobiomicslab Skill

Use when when you need to visually compare two or more spectra (MS1, MS2, or extracted ion chromatograms) across different retention times, m/z ranges, or ion mobility bins in a single figure. Apply this skill after extracting spectra arrays from MZA files (e.

holobiomicslab Skill

Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment masses.

holobiomicslab Skill

Use when you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect misalignment of feature groups.

holobiomicslab Skill

Use when when you have a computational simulation framework (e.

holobiomicslab Skill

Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint data into a single matrix for comparative analysis.

holobiomicslab Skill

Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by matching experimental spectra against a database of predicted post-translationally modified RiPP structures derived from.

holobiomicslab Skill

Use when after peak picking has been completed on INADEQUATE NMR spectra and you need to group correlated peaks into compound-specific networks before matching against a metabolite database.

holobiomicslab Skill

Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans, and fragmentation events in memory.

holobiomicslab Skill

Use when when you have two MS/MS fragmentation spectra (with precursor m/z values and fragment ion lists) and need to establish correspondence between their fragment ions beyond simple pairwise comparison.

holobiomicslab Skill

Use when you have picked peaks (coordinates and intensities) from an INADEQUATE NMR spectrum and need to cluster them into networks representing individual compounds.

holobiomicslab Skill

Use when when importing raw mass spectrometry data in formats like mzML, mzXML, msp, MGF, or JSON and you need to ensure spectral data quality before proceeding to similarity comparisons or other downstream analyses.

holobiomicslab Skill

Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry experiment (e.g., via USI) and before intensity filtering or scaling.

holobiomicslab Skill

Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.

holobiomicslab Skill

Use when when you have a large MsBackend object and need to (1) select a contiguous or non-contiguous range of spectra for focused analysis, or (2) combine spectra from multiple independently-loaded backends (e.

holobiomicslab Skill

Use when when you have downloaded and extracted a GNPS archive (from GNPS1 or GNPS2 workflows) and need to establish which spectral records (from spectra.mgf) were generated from which bacterial strains or samples. The file_mappings.tsv or file_mappings.

holobiomicslab Skill

Use when you have SWATH-MS raw data (mzML or vendor format) from an untargeted metabolomics experiment and need to identify metabolites.

holobiomicslab Skill

Use when you have a large collection of tandem mass spectra (mzML, mzXML, or MGF format) and want to group similar spectra into clusters to identify redundancy, discover novel peptides or metabolites, or prepare data for downstream annotation.

holobiomicslab Skill

Use when when a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification. Apply this skill after loading the mwTab file using the mwtab parser but before quality assurance sign-off or deposition to the Metabolomics Workbench.

holobiomicslab Skill

Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.

holobiomicslab Skill

Use when when you have raw mzML or mzXML files containing uncompressed m/z and intensity arrays and need to load spectra into a uniform data contract before compression, cross-format comparison, or algorithmic processing.

holobiomicslab Skill

Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or enable CCS correction by comparing measured lipids against known library entries with validated CCS values.

holobiomicslab Skill

Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.

holobiomicslab Skill

Use when you have: (1) a set of predicted candidate metabolites with known mass-to-charge ratios and chemical properties derived from a parent drug formula; (2) raw mass spectrometry data in mzML format from a sample suspected to contain those metabolites;

holobiomicslab Skill

Use when when you have a known drug's chemical formula and need to generate a comprehensive list of predicted metabolite formulas to match against experimental mzML mass spectrometry data.

holobiomicslab Skill

Use when you have at least 3 raw mass spectrometry samples in open formats (mzML, mzXML, CDF) from untargeted metabolomics experiments and need to configure parameters for XCMS, MZmine2, or similar processing software.

holobiomicslab Skill

Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to chemodiversity analysis, transformation network generation, or multivariate statistics.

holobiomicslab Skill

Use when when you need to empirically validate that one mass spectrometry data processing library achieves higher throughput than competing alternatives. Specifically: you have multiple candidate libraries (e.

holobiomicslab Skill

Use when after running SIRIUS on a mass spectrometry feature set and obtaining compound_identification.tsv output containing Zodiac and Cosmic confidence scores, apply this filter to eliminate low-confidence SIRIUS annotations before downstream prioritization or chemical class analysis.

holobiomicslab Skill

Use when when you need to retrieve m/z–intensity pairs from a MsBackend-backed Spectra object for visualization, comparison, or processing; particularly when the backend stores peak data separately (e.

holobiomicslab Skill

Use when when you have raw mass spectra from experimental libraries (e.