Use when you have a recalibrated FT-ICR mass spectrum (Bruker .d format or equivalent) with detected, noise-thresholded peaks and need to assign chemical formulas to each peak.
Use when when you need to work with mzMLb (HDF5-based) proteomics data in pyteomics and want to confirm that the required h5py and hdf5plugin libraries are installed and…
Use when you have execution-time metrics (from a benchmark table or profiling logs) across multiple visualization backends for the same set of plots (e.
Use when when you have paired spatial transcriptome and metabolome datasets in h5ad format with spatial coordinate matrices (obsm['spatial']) and you need to establish spot-level…
Use when after LDA topic inference has assigned dominant topic labels to mass spectra, and before those labels are passed to MLP or GNN multi-task training.
Use when training a DNN on retention time prediction or similar continuous regression tasks where: (1) the feature space is very high-dimensional (thousands of molecular…
Use when after imputing missing values and before assigning Cluster_IDs in the notame preprocessing pipeline.
Use when when setting up HiC-Pro or similar multi-tool pipelines where tool availability and version constraints are prerequisites for downstream analysis.
Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference…
Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts,…
Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform…
Use when you have preprocessed, statistically significant LC-MS features (from multiple assays or a single assay) and need to group features that represent the same metabolite in…
Use when you have normalized abundance data from LC-MS/MS for multiple samples classified into three or more discrete groups (e.
Use when when you have peak area tables (unlabeled C12 and labeled C13) from LC-MS metabolomics with sample metadata indicating case and control groups, and you need to…
Use when xCMS grouping has been performed on LC-MS data from studies with hundreds of samples or data acquisition periods longer than a week, where retention time drift structures…
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.
Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into…
Use when you have a normalized matrix of feature attribution scores (microbes × metabolites) derived from a trained neural network, and you want to partition both microbes and…
Use when you need to quantify the degree of match between two MS/MS spectra—either
Use when you have trained MLPNN models on paired microbiome-metabolome data (via 10-fold cross-validation repeated across multiple iterations) and need to derive interpretable…
Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings.
Use when you have exported lipid identifications from MS-DIAL (version 4 or 5) and need to run LipoCLEAN quality filtering on that output.
Use when when designing injection plate layouts in InjectionDesign and needing to display sample positions with clear, domain-appropriate labels on the y-axis (e.g., row…
Use when you have a trained formula ranking model (such as MIST-CF) and want to measure the specific performance gain from incorporating multiple positive-mode adduct types (e.g.,…
Use when you have run ORA on simulated metabolite sets with known null conditions (no true pathway enrichment) and need to measure how detection coverage, pathway database size,…
Use when when you have resolved mzML or mzXML spectrum files and need to isolate signals for a target m/z value (e.g., 870.954) across all retention times or a specific scan.
Use when when you have multiple CDF files from mass spectrometry imaging experiments (e.g., root tissue MALDI-MS data) that need to be ingested into Matlab for linear imaging…
Use when you have GNPS-style MGF spectral files as input and need to run Mass2SMILES MS/MS-to-structure inference without installing TensorFlow, CUDA, or Python dependencies…
Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally modified variant of that compound—and you need to identify which atoms in — from…
Use when you have m/z values from mass spectrometry imaging (or similar MSI experiments) and need to assign molecular formulae to them.
Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensities) and aim to predict functional pathway activity without explicit — from…
Use when you have GNPS-style MGF spectral files from MS/MS experiments and need to predict the molecular structure (as SMILES) of unknown compounds.
Use when after drift correction in non-targeted LC-MS metabolomics workflows, when you need to decide which molecular features are sufficiently reproducible (low instrument/QC…
Use when you have tandem MS/MS spectrum data in standard peak file formats (mzML, mzXML, or MGF) and need to cluster spectra based on precursor mass and fragment ion similarity.
Use when you have generated or assembled a lipid spectral library with precursor m/z values, adduct information, and fragmentation patterns, and you need to import those spectra…
Use when you have a metabolite intensity matrix (rows=metabolites or peaks, columns=samples) paired with metabolite-to-pathway or metabolite-to-feature-group annotations, and you…
Use when when you need to programmatically interface with a TensorFlow Serving model instance and must discover or validate the expected input names (e.
Use when when importing raw mass spectrometry data from instrument vendors or public repositories in one format (e.g., mzML, mzXML) and needing to export it in another format (e.
Use when when you have a retention-time dataset (e.g., SMRT or Eawag_XBridgeC18_364)
Use when when you have matched transcriptomics (RNA-seq read counts), intracellular metabolomics (LC-MS abundance data), and extracellular flux measurements (YSI bioanalyzer or…
Use when you have an experimental MS/MS spectrum (m/z and intensity pairs in mzML/mzXML format from DDA or targeted acquisition on Thermo, Waters, or Bruker instruments) and need…
Use when after peak detection in a nontargeted LC-MS workflow when you have a feature table with detected peaks and need to filter low-quality features or understand why certain…
Use when you have LC-IM-MS/MS raw data from sterol-containing tissue samples and need to assign detected peaks to specific structural isomers (e.g., distinct double bond positions…
Use when you have one or more MS/MS spectra in .mgf format (or USI identifiers) and need to: (1) identify unknowns by searching against domain-curated reference data; (2) assign…
Use when you have a GC-MS dataset with multiple sample files (e.g., Std_soln_00,
Use when you have an ArchR project object with dimensionality reduction results (LSI or combined dimensions from scATAC-seq ± scRNA-seq) and want to infer pseudotime trajectories…
Use when you have a negative-mode or positive-mode LC-MS feature table with observed m/z values and peak intensities, and you need to identify which metabolites (by KEGG ID) are…
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
Use when you have cloned the GNPS_MASST codebase and need to instantiate a domain-specific MASST variant (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) to…
Use when when you have raw ion mobility-mass spectrometry data (drift times, m/z values, and frame metadata) from DTIMS-MS, TWIMS-MS, or SLIM-based instruments and need to compute…
Use when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to…
Use when you have raw or converted spectral data (jcamp, RAW, or mzML format) from NMR, IR, or MS instruments and need to identify individual peaks, extract their properties…
Use when after applying CordBat batch correction to a log2-transformed metabolite matrix from multi-batch metabolomics data, you want to quantitatively and visually assess whether…
Use when you have computed frequent fragmentation patterns from a collection of MS/MS spectra using mineMS2, and you want to focus pattern interpretation on subsets of spectra…
Use when you have raw Hi-C FASTQ files from a sequencing experiment and need to generate kilobase-resolution Hi-C contact maps conforming to ENCODE reference standards.
Use when when applying a pre-trained Word2Vec model to mass spectra at inference time (e.g., library matching or molecular networking), especially when the query spectra may…
Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and…
Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans,…
Use when after simulating and convolving individual metabolite multiplets with realistic lineshapes (Lorentzian or Gaussian) and combining them into a single time-domain FID array.