Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains…
Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown…
Use when you have acquired one or more tandem MS/MS spectra and need to identify metabolites against a reference library filtered by biological domain (e.
Use when after scipy.signal.find_peaks has identified candidate peaks on a composite mass track segment, evaluate each peak to decide whether to retain it in the final feature…
Use when you have raw LC-HRMS profile-mode data and need to identify candidate chromatographic peaks before classification or feature extraction.
Use when after instantiating a specXplore dashboard session layer with a loaded session data object from disk, before conducting visual exploration of LC-MS/MS spectral data.
Use when you have paired metabolomics data (MS/MS spectra and feature quantification) linked to organismal or tissue taxonomy, and you want to reduce false positive annotations…
Use when after executing multidimensional smoothing, spike removal, or saturation repair on raw TOF-MS or IM-MS data (.d format from Agilent MassHunter) to confirm that signal…
Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
Use when when you have a set of molecules with known chemical structures and need to prepare them for classification or prediction tasks.
Use when your XCMS-processed LC-MS dataset exhibits retention-time drift or misalignment artifacts—particularly when analyzing hundreds of samples, data acquisition spans longer…
Use when you have raw or processed TWIM-MS data (arrival time and m/z pairs) from multiple lipid, protein, or metabolite classes and need to classify features by biomolecular type…
Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the…
Use when when you need to reproduce or validate a specific historical release artifact (e.g., a Semantic Release v1.0.
Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained…
Use when when you have a list of chemical compounds (with m/z values, retention times, and intensities) and need to simulate their acquisition behavior under a specific ionization…
Use when your MSI data is stored in a Cardinal imaging experiment object (version 2.2+) that has already been peak-binned with peakBin(), and you want to run mass2adduct's…
Use when you need to confirm that a documented web service URL is live and reachable before attempting to submit analysis jobs, download results, or integrate the service into an…
Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with…
Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real…
Use when when you have untargeted GC–MS or LC–MS data in the form of a two-dimensional m/z vs retention time map and need to identify marker features without conventional peak…
Use when you have downloaded raw spectroscopic data files (NMR, HSQC, COSY, IR modalities) from the Zenodo repositories and need to convert them into the standardized multi-modal…
Use when after importing fragment files into AnnData using pp.import_fragments and before performing spectral embedding (tl.spectral) or other dimension reduction.
Use when when you have tandem mass spectra from ribosomally synthesized peptides (RiPPs) and suspect the presence of unknown or non-standard post-translational modifications that…
Use when you have raw LC-MS data in mzML or mzXML format and need to extract reproducible, high-quality metabolite features (m/z, retention time, intensity) for global…
Use when converting raw MS/MS spectra from library files (e.g., .msp format) into structured library entries, or when annotating experimental LC–MS features against fragment…
Use when when you have seed metabolite structures (SMILES or MOL format) from metabolomics data and a curated biotransformation rule database (each rule specifying reactant…
Use when you have evaluated a parametric denoising strategy (e.g., frequency-based
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…
Use when you have trained a neural network or regression model on one paired microbiome-metabolome dataset and wish to test whether it can predict metabolite abundances in an…
Use when after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature…
Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.
Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
Use when after training a neural network or regression model to predict metabolomic profiles from microbiome data.
Use when you have latent low-dimension peak features extracted by a Graph-attention
Use when when exporting quantified MSI data (feature-by-pixel intensity matrices with associated ion m/z, lipid annotations, and pixel spatial coordinates) from LipidQMap and you…
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 after imputing missing values and before assigning Cluster_IDs in the notame preprocessing pipeline.
Use when you have transcript-level abundance, count, and length estimates (from salmon, Sailfish, or kallisto via tximport) and want to perform gene-level differential expression…
Use when when you have an unknown metabolite compound with mass spectral data, have retrieved candidate structures from a molecular structure database (PubChem, HMDB), and have…
Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.
Use when after anchor selection and retention-time spline mapping have produced a candidate list of feature pair alignments, but before final scoring and reduction of the combined…
Use when when you need to compare the computational efficiency of different mass spectrometry libraries on identical data and processing pipelines, or when you want to establish…
Use when after training multi-layer perceptron neural networks via cross-validation
Use when when you have raw or lightly processed 1D NMR spectra (¹H and/or ¹³C) from unknown organic compounds and need to extract latent spectral features prior to structure…
Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays
Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify…
Use when when implementing or auditing a deep learning pipeline for MS/MS-based molecular formula prediction, verify that precursor m/z values in the input feature array are…
Use when you have developed or adapted a peak detection method for chromatography–mass
Use when after constructing a kNN graph (via pp.neighbors) on preprocessed, scaled, and PCA-reduced single-cell expression data.
Use when you have raw or preprocessed electron ionization (EI) mass spectral data that must be stored in, retrieved from, or validated against the MSP file format (used by NIST MS…
Use when you have aligned MS/MS feature tables (e.g., from MSDial ver. 4.80) representing unknown metabolites suspected to be Phase I/II transformation products of xenobiotics,…
Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or…
Use when you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
Use when after constructing a network graph where nodes represent Mass2Motifs (or spectra) and edges encode pairwise spectral similarity scores, and you need to export the network…
Use when immediately after automatic peak detection on a raw or processed MS spectrum when you have a list of candidate peaks with m/z and intensity values but lack systematic…
Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1…
Use when you have tandem mass spectra data and need to predict a discrete molecular property (e.g., presence/absence of a sulfo group) while maintaining full interpretability of…
Use when after cluster-based filtering has produced a set of candidate KEGG compounds for each feature cluster in untargeted LC-MS data, and you need to rank these candidates by…
Use when after executing a Nextflow-based LC-HRMS metabolomics workflow with Docker or Singularity containerization on .mzML LC-MS data, before proceeding to downstream…