Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata…
Use when validating project JSON documents against the platform's schema (app/public/schema.json) and you need to ensure all URL-type fields conform to URL syntax rules.
Use when when fitting a nonlinear regression (GAM spline) through retention time anchor points derived from feature pair alignments in LC-MS metabolomics, and you suspect some…
Use when you have selected a subset of public tandem MS files from ReDU/MassIVE that have been processed through GNPS spectral library matching, and you need to organize their…
Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
Use when you have a feature table from LC-MS data alongside blank (solvent-only) sample runs, and you want to remove features whose intensity in study samples is not substantially…
Use when you have an untargeted metabolomics feature table (m/z and retention time columns) and a statistical test result (p-value) per feature, but lack confident metabolite…
Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in…
Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision…
Use when you have a collection of compound structures in SDF format (e.g., DNA adduct structures) and need to systematically generate predicted fragment spectra across a defined…
Use when a Shiny application or R-based tool is known to run on only one operating system (e.g., Windows-only), and you need to identify the root causes preventing execution on…
Use when before submitting peak data or other inputs to a machine learning classification API for the first time, after a model update, or if you encounter unexpected prediction…
Use when you have raw LC-MS data (mzML or vendor format) and need to discover and characterize all chromatographic features present, without prior knowledge of target analytes.
Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a…
Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal…
Use when you have a spatial omics dataset (AnnData object with coordinate columns like 'x', 'y', 'z') and an associated tissue image file (e.g., TIFF, PNG, or HE-stained…
Use when when integrating an R package that wraps a compiled .NET assembly (such as rawrr), you need to verify that the internal dispatch mechanism between the R layer and the C#…
Use when after enriching a project JSON document with external metadata (e.g., organism names, genome identifiers) or before writing enriched JSON to disk.
Use when you have untargeted MS2 spectral data (in MS2MP-compatible format) and need to assign KEGG pathway annotations to unknown metabolites.
Use when when preparing a software release, testing contribution workflows, or auditing package availability: verify that matchms can be installed and imported successfully from…
Use when your research proposes a new spectral embedding, matching algorithm, or retrieval method and you need to quantify its improvement over known baselines.
Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
Use when you have experimental retention times measured on a source chromatographic
Use when you have raw lipidomic and metabolomic spectral data files from a Multi-ABLE barocycler-based concurrent multiomics experiment and need to normalize ion intensities,…
Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined…
Use when your research involves searching MS/MS spectra against multiple curated taxonomic or domain-specific databases (microbial, plant, tissue, microbiome, or food origin) and…
Use when removing invalid or malformed entries (e.g., SMILES validation, format errors) from large spectral datasets (GNPS, MoNA, MTBLS1572, MassBank).
Use when you have transcript quantification output (TPM or raw counts) from a pseudo-aligner (Salmon or kallisto) and an ioe/ioi event definition file from SUPPA2's generateEvents…
Use when when you have mass spectrometry spectra in one of the six supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to convert them to a different format…
Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly…
Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings…
Use when you have raw ion images from MSI data and need to train a contrastive encoder to learn stable, mode-specific representations.
Use when you have raw metabolomics data in mzML or mzXML format and need to extract ion features, align them across samples, and produce a normalized feature table for downstream…
Use when deploying the ipbhalle/metfragweb container and you need to supply custom MetFrag settings (ChemSpider tokens, proxy servers, local database connections) without…
Use when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow…
Use when you have MGF or native MS/MS arrays (mz_array, intensity_array, precursor_mz, adduct) and want to predict the most likely molecular formula.
Use when when preprocessing a public MS/MS spectral library (e.g., GNPS) for machine learning and you discover discrepancies between expected and observed compound counts after…
Use when you have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level…
Use when when you have CE-MS raw data (mzML or netCDF format) with extracted ion traces for target compounds and need to identify peak boundaries and extract quantitative peak…
Use when after running DESeq() to fit negative binomial GLMs and obtaining raw p-values from results(dds), when you need to reduce false positives from multiple testing across…
Use when you have pairs or triplets of MS/MS spectra with associated metadata (compound structural information, Tanimoto similarity scores) and want to learn embeddings that…
Use when you have a peak table from XCMS preprocessing with intensity measurements for the same set of metabolites across multiple QC replicate injections (samples marked…
Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate…
Use when xCMS alignment produces suspected misaligned feature groups across hundreds of samples or long acquisition runs (>1 week), particularly when global XCMS warping functions…
Use when you have identified one or more proton NMR spectral regions-of-interest
Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and measured CCS values need bias assessmen — from…
Use when you have raw or annotated MS/MS spectra (in MGF, mzML, or mzXML format) destined for de novo peptide sequencing with Casanovo.
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 you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass…
Use when you have aligned ATAC-seq BAM files from Tn5-based chromatin accessibility assays and need to perform footprinting analysis.
Use when you have executed a spectrum search against one or more domain-specific
Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names…
Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected)
Use when when you have a set of candidate LC gradients (parameter combinations) that you wish to evaluate with a Gaussian process model, or when you need to convert raw gradient…
Use when when you have raw tandem mass spectra in mz/intensity format with precursor m/z values, and need to extract all fragmentation features (observed peaks and neutral losses)…
Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per…
Use when adding a new converter class to MSMetaEnhancer or when modifying an existing converter's __init__ method to add/remove conversions.
Use when when validating a new or reimplemented quantification tool against a reference implementation on the same dataset and index, or when investigating whether changes to seed…
Use when building a transformer-based neural network for chemical formula ranking or classification from mass spectrometry spectra, and you need to encode categorical chemical…