Use when you have raw mass spectrometry data in mzML or Bruker .d format and need to ingest it into a tabular format (pandas DataFrame) for visualization, statistical analysis, or…
Use when after acquiring MS/MS spectral data from untargeted metabolomics experiments and having candidate transformed structures from biotransformation rule application.
Use when you have extracted a peak list from MSI data and need to annotate matrix-related signals, but overlapping peaks or isobaric ions (ions with identical or near-identical…
Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers…
Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON…
Use when you have generated gene-level count matrices via two methodologically distinct routes—e.
Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and…
Use when after clustering features with RAMClustR and inferring molecular weights via do.findmain, when you need to perform structure elucidation or molecular formula prediction…
Use when you have raw gas or liquid chromatography–mass spectrometry data (in NetCDF or mzML format) and need to detect features, align them across samples by retention time and…
Use when when extracting and validating chromatographic peaks for target molecules from centroided mzML files, particularly when working with multiple isotopologues and adducts…
Use when you have a matrix of Nightingale Health 1H-NMR metabolomics measurements (samples × features) and need to generate predicted metabolic scores published in peer-reviewed…
Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that…
Use when you have a baseline GNN model for predicting a continuous molecular property (e.
Use when you have spatial molecular data (e.g., coordinates from microscopy or sequencing assays stored in an AnnData object), you need to compute a k-nearest-neighbor graph for…
Use when when converting MS/MS spectra into spectral documents for Spec2Vec embedding, and you want to capture chemical relationships implicit in the fragmentation pattern (e.g.,…
Use when when you have a Spectra object backed by an on-disk MS data source (e.g., MsBackendMzR reading mzML, mzXML, or CDF files) and need to process large numbers of spectra in…
Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS…
Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR…
Use when you have structural input data (SMILES or molecular geometry files) for N-Me derived unsaturated sterol lipids and need to generate a predicted CCS dataset indexed by…
Use when extracting migration times of specific analyte or reference markers (e.g., Paracetamol EOF marker) from CE-MS files using peak-picking workflows.
Use when you have normalized peak intensities or abundance matrices from mass spectrometry (e.
Use when you have raw MS/MS peak lists and suspect electronic noise contamination—particularly
Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries…
Use when when you have raw GC–MS or LC–MS data (m/z vs retention time chromatography-mass spectrometry maps) and need to identify analyte signals and marker features without…
Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
Use when processing extracted peak lists from MSI data and you need to annotate matrix-related signals but suspect that multiple ions with the same or very similar m/z values…
Use when you have centroided mzML LC–MS data, a curated list of target compounds (with theoretical m/z, expected retention time, and polarity), and you need to confirm target…
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 mass tracks have been aligned across samples into a MassGrid structure (m/z-aligned, same mass-to-charge ratio) and retention time calibration dictionaries — from…
Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format with mandatory PRECURSOR_MZ and IONMODE tags) and need — from…
Use when you have a peak-intensity matrix from untargeted LC-MS analysis (raw detected peaks with m/z and intensity values) and need to assign putative metabolite identities.
Use when after computing Multi-Block Variable Importance in Projection (MB-VIP) scores on a fitted MB-PLS discriminant model, when you need to distinguish signal features from…
Use when you have extracted fragmentation patterns from a collection of MS/MS spectra (using mineMS2) and have partitioned spectra into components via GNPS molecular networking…
Use when you have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and…
Use when you have observed mapping rate or quantification disagreement (e.g., >0.1% divergence in mapping rate or Pearson r < 0.
Use when you have computed pairwise similarity or mass difference scores between all fragment ions across two tandem mass spectra and need to select the non-overlapping set of ion…
Use when when you have curated or synthesized a set of custom lipid species (e.g., rare or organism-specific lipids, modified lipids, or synthetic standards) and need to integrate…
Use when when performing transcript- or gene-level differential expression analysis and your quantification tool (Salmon, Sailfish, or kallisto) has produced Gibbs sample or…
Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
Use when you have a normalized abundance matrix from LC-MS/MS profiling with sample class assignments (e.g., phenotypic groups, disease states, treatment conditions) and need to…
Use when your annotation pipeline depends on multiple external web converters and you need to diagnose why annotation jobs are failing, slow, or incomplete.
Use when you have paired-end ChIP-Seq data (BEDPE format) and need to determine the empirical fragment length (insertion length) before peak calling.
Use when when you have a GitHub-hosted Python project (or other supported language) with an existing test suite and want to gate code contributions on multiple quality dimensions…
Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or…
Use when when evaluating whether a mass spectrometry analysis platform (such as mzmine) has comprehensive module support across multiple ionisation and separation techniques (LC,…
Use when you have a Thermo Fisher Orbitrap .raw file and need to retrieve a specific scan's spectral data (m/z and intensity arrays), validate instrument parameters (resolving…
Use when when you have raw mass spectrometry transition data from a triple-quadrupole
Use when deploying Mass2SMILES on a TensorFlow-CPU build and you need to optimize inference throughput on multi-core systems.
Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES),…
Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or…
Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined…
Use when after normalization (normalize_total, log1p transformation) and before PCA or other dimensionality reduction on raw or near-raw single-cell gene expression matrices.
Use when processing IM-MS data files (Agilent .d or UIMF format) that contain high-abundance ions suspected of signal saturation, particularly in untargeted or discovery…
Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both…
Use when after peak filtering (by m/z, isotopic presence, formula assignment error, and sample prevalence) and before multivariate analysis (PCA, NMDS, PERMANOVA) when comparing…
Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality.
Use when when you have a calibrated FT-ICR mass spectrum (e.g., ESI-NEG mode) and need to decide between rapid single-assignment (first_hit=True) and exhaustive multi-assignment…
Use when when fitting a multi-block PLS discriminant model on multi-assay LC-MS metabolomics data and you need to determine the number of latent variables to retain without…
Use when you have extracted a chemical mixture from a real mzML acquisition (e.g., Beer1pos), simulated the same chemicals through ViMMS using a chosen controller (e.
Use when after GNPS spectral library search has returned matched chemical annotations (with m/z values and cosine similarity scores) for MS/MS spectra.