Use when you have extracted tabular data (e.g., protocol descriptions, sample preparation steps) into an intermediate JSON representation and need to subset records by type or…
Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to…
Use when when baseline MLP or GNN models for spectral prediction show limited performance on metabolite annotation tasks, and you have access to auxiliary spectral topic labels…
Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all…
Use when you have predicted peptide sequences from a de novo sequencing tool (e.g., Casanovo) and want to understand the fine-grained accuracy of the predictions beyond…
Use when a user submits one or more MS/MS spectra (via .mgf file, USI list, or direct upload) and the downstream analysis requires dispatching to a specific domain-specific MASST…
Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to…
Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).
Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic…
Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships…
Use when you have raw LC/MS data in mzML format and your analysis goal is to comprehensively detect and annotate all mass spectral features present, rather than measuring…
Use when raw NetCDF-format GCxGC-MS chromatograms exhibit steady or increasing baseline intensity caused by instrumental contamination, column bleeding, or thermal drift;
Use when when you have trained multiple regression models (e.g., using different feature sets: descriptors-only, fingerprints-only, or combined) on the same training data and need…
Use when during the LDA training phase when you need to decide whether the model has learned a stable representation of Mass2Motifs.
Use when when analyzing imaging mass spectrometry datasets where you need to reduce high-dimensional peak intensity features while preserving spatial structure, and when automatic…
Use when after autoQ has extracted isotopologue peak area measurements from mz(X)ML files and you need to prepare the integrations data frame for visualization with metBarPlot or…
Use when when you have a normalized metabolite abundance matrix with sample metadata assigning each sample to one of three or more distinct biological classes (e.
Use when after anchor selection and RT mapping spline fitting, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to determine which…
Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate) and need to find their -matched structural analogues within a reference library — from…
Use when ingesting mass spectrometry spectra from heterogeneous databases or libraries where adduct annotations may be incomplete, incorrectly formatted, or inconsistent with the…
Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z…
Use when after XCMS feature detection, grouping, and retention time correction when you have aligned features with consistent retention times and intensity patterns across samples.
Use when you have a mass spectrum of an unknown metabolite with a known or inferred precursor m/z, you have run a deep-learning semantic similarity model (e.
Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you need to reduce data volume while preserving s — from…
Use when you have a parsed sample list with metadata (sample IDs, classification
Use when you have mzPeak files (Parquet-based archives containing mass spectrometry spectra and chromatogram data) that you want to analyze in R, and you need to convert the Arrow…
Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared…
Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each…
Use when you have raw mass spectrometry data in vendor-proprietary formats (e.g., .raw, .d, .ms) that you need to upload to MassIVE for public sharing or submit to GNPS for…
Use when when you have IM-MS lipidomics data acquired on samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and need to quantify systematic CCS bias…
Use when when you have built a new tool implementation or major version and need to verify it produces equivalent results to a reference implementation on the same input data and…
Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for…
Use when after initial retention-time-based feature grouping (e.g., ±20 s window) when you need to separate co-eluting features that are chemically distinct.
Use when you have a validated or curated dataset (e.g., a TSV or gzip-compressed
Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing.
Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic…
Use when after fitting a Gaussian Process regression model to prior LC-MS gradient runs (retention times, separation efficiency scores, or compound identification counts) — from…
Use when you have a trained graph neural network model for CCS prediction and need to identify which molecular structural features drive individual predictions or systematic…
Use when you have a metabolite intensity matrix (samples × metabolites) with assigned annotations (peak IDs mapped to KEGG or ChEBI compound IDs), a metabolic pathway database,…
Use when after batch effect removal and sample integration, when you have a normalized feature-by-sample abundance matrix (finalData) with corresponding sample group labels…
Use when when you have a collection of MS/MS reference spectra and unknown query spectra that must be rapidly matched against a large spectral library, and you need to enable…
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 you have a chromVARDeviations object with precomputed bias-corrected deviations and z-scores for multiple annotation sets (e.
Use when you have LC-MS feature tables (with m/z and retention time columns) paired with raw .mzXML or .mzML files, and you need to automatically validate which detected features…
Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and…
Use when when you have query chemicals identified by GC-MS (with Match.Factor values) and need to verify structural similarity against a reference chemical library to confirm…
Use when after computing deviations for both motif and kmer annotations on the same chromVAR dataset, when you need to determine whether kmers and motifs are redundant predictors…
Use when you have a cooler Hi-C contact matrix, a set of genomic features (e.g., CTCF peaks, enhancers, or TAD boundaries defined in BED format), and want to quantify average…
Use when you need to determine the complete set of validated instrument/vendor and acquisition mode combinations for a mass spectrometry analysis tool, when assessing whether your…
Use when you are designing a new backend or data container that must integrate seamlessly with an existing Spectra-based workflow. You have identified a virtual parent class (e.
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 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 after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
Use when when setting up matchms for the first time in a new environment, after upgrading Python or conda, when switching between package managers (pip vs conda), or when…
Use when when you need to capture a snapshot of a research software project's health metrics from multiple CI/CD and repository services (Travis CI, Landscape.
Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine,…
Use when when you have molecular structures encoded as SMILES strings and need to incorporate them into a multi-modal language model (such as BART) that also processes mass…
Use when preparing ion image data for contrastive learning in mass spectrometry imaging (MSI), specifically when you need to augment single ion images into pairs of variants for…
Use when after extracting tabular data into intermediate JSON representation (via tagging), or after manual JSON editing, and before converting to a target format (e.g., mwTab for…
Use when you need to build a comprehensive EI spectral reference library for GC-MS compound identification in MS-DIAL, starting from raw downloads of NIST, RIKEN, MoNA, or SWGDRUG…