Use when when you have ionized adduct structures (in SMILES or MOL format) from an upstream ionization-state determination step and need to produce multiple low-energy 3D…
Use when you have raw quantification data (abundance or intensity values across samples and features) from mass spectrometry or similar high-dimensional assays and need to prepare…
Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a…
Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its metabolic fate across one or more biological systems.
Use when you have raw MS/MS spectra (in MGF or mzML format) with unscaled peak intensities and noise artifacts, and you plan to rank chemical formulas, predict adducts, or score…
Use when you have raw MS/MS spectra in multiple formats (.mgf, .msp, .mzML) that contain background noise, instrument artifacts, or low-abundance fragments that would degrade…
Use when when you have a Thermo Scientific .raw file from an Orbitrap instrument (e.
Use when when you have paired MS/MS spectra with known structural similarity labels (Tanimoto scores from molecular fingerprints) and need to predict structural similarity for new…
Use when when you have an LC-MS feature table with m/z and retention time columns and need to identify which observed ions correspond to the same neutral compound under different…
Use when after computing a correlation matrix (e.g., Pearson correlation across samples) on statistically significant LC-MS features, particularly when you need to inspect…
Use when you have a collection of preprocessed mass spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to quantify similarity relationships across all pairs—for instance,…
Use when you have a feature table with intensity values across study (unknown) and blank control samples, and you need to remove features that may represent instrument artifacts,…
Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you…
Use when when you have molecular structures, a regression target (e.g. retention time), and want to establish whether one class of molecular features (e.g., fingerprints)…
Use when when you have computed PCA coordinates from chemical annotation matrices (e.
Use when when designing or optimizing an MsBackend implementation (or similar columnar data structure) you must decide whether to pre-allocate all known columns in the backing…
Use when you have two or more feature tables in HDF5 format with detected peaks characterized across multiple dimensions (mz, drift_time, retention_time, intensity) and need to…
Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
Use when you have one or more MS/MS query spectra (in mzML, mgf, msp, mzxml, json, or pickled matchms format) and a pre-built spectral library stored in SQLite with precomputed…
Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators)…
Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g.,…
Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction.
Use when you have normalized peak intensity data (or absence/presence matrices) from metabolomics experiments with multiple samples and need to quantify compositional differences…
Use when after successfully resolving a USI string to a specific mass spectrum scan, and before performing spectral matching, library search, or comparative analysis.
Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra (as numerical arrays or feature tensors) from an unknown organic compound with ≤19 heavy atoms, and you need to predict…
Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and…
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…
Use when you have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation…
Use when after calling squidpy.gr.spatial_neighbors or any graph-building operation that outputs sparse matrices to adata.
Use when when processing LC-MS peak tables from isotope tracing experiments where multiple ionization adducts ([M+H]+, [M+Na]+, [M+NH4]+, etc.) and in-source fragments have…
Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredic — from…
Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5)
Use when you have a collection of raw mass spectrometry data files from multiple instrument vendors (Agilent, Bruker, Thermo) and/or mzML exports that need to be converted to a…
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…
Use when you have untargeted MS2 spectral data (in MS2MP-compatible format) and need to assign KEGG pathway annotations to unknown metabolites.
Use when you have a large gene expression matrix (e.g., thousands of genes) from normalized microarray or RNA-seq data and need to reduce computational burden before running…
Use when you have a pre-trained DNN model for retention time prediction and need to adapt it to a new chromatographic method or instrument where you have only 10–20 calibration…
Use when you have a tandem mass spectrum with observed m/z peaks and a known peptide sequence (as a ProForma string, optionally with post-translational modifications), and you…
Use when you have real mzML LC-MS/MS data (e.g., from a Beer sample or HMDB reference set) and want to test whether a proposed TopN DDA strategy (or variant) can accurately…
Use when after submitting a POST request to the /api/smart3/search endpoint with peak data as a JSON payload, you receive an HTTP response and need to extract classification…
Use when when performing gene-level differential expression analysis on RNA-seq data where samples may express different isoforms of the same gene at different relative…
Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment…
Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links…
Use when when you have read LC-MS peak table data from Excel (or equivalent) into R and need to organize it into a structured object that tracks feature abundances, sample…
Use when when you have imported a tab-delimited metabolomics file (via readData or similar) containing columns for compound identifiers, sample/aliquot names, peak areas (primary…
Use when you have consensus metabolic reconstructions for multiple community members (e.g., plant-associated microbes or plant-microbial consortia) and those individual models…
Use when you have raw or normalized single-cell RNA-seq expression data stored in an AnnData object (`.h5ad` format) and your analysis goal is to infer developmental or…
Use when your input is a raw two-dimensional MS map (m/z vs retention time) derived from chromatography–mass spectrometry data with poor signal-to-noise characteristics, and you…
Use when when preprocessing raw SMILES strings from external chemistry databases (e.g., CCSBase, METLIN-CCS, or custom compound libraries) that may contain multiple valid but…
Use when you have raw line-scan mass spectrometry imaging data from nano-DESI or other line-scan acquisition modes and need to produce a georeferenced 3D pixel array.
Use when you have raw LC-MS data (mzML or equivalent format) from a metabolomics experiment and need to extract a reproducible, quantified feature table with intensity…
Use when when applying a pre-trained Spec2Vec Word2Vec model to new mass spectra (particularly those outside the model's training distribution), you need to assess whether peaks…
Use when you need to verify claims about algorithm performance, data processing correctness, or workflow outcomes in a scientific article or software repository.
Use when when you have raw or GNPS-processed MS2 spectral data from microbial strains and need to organize spectra into molecular families (grouped by spectral similarity) while…
Use when after peak picking across individual spectra in an MSImagingExperiment,
Use when you have two or more CSV feature tables from separate metabolomic experiments (each containing mass, retention time, intensity, isotope, and adduct columns), and you need…
Use when when you have a GC-MS dataset (CSV with columns: Component.RT, Component.Area, Base.Peak.MZ, File.Name, Compound.Name, Match.Factor) and a known set of target chemicals…
Use when you have variable-length MS/MS peak lists (m/z arrays and intensity arrays) that must be fed into a transformer architecture for tasks like compound identification or…