Use when when you have processed LC-MS/MS spectral data in .mgf format with precomputed ms2deepscore similarity matrices and need a 2-D overview representation that preserves…
Use when working with raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains low-abundance background noise, isolated high-intensity artifacts, or jagged peaks…
Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a…
Use when you have completed XCMS grouping on LC-MS data and suspect misaligned features due to long acquisition periods (>1 week) or large sample cohorts (hundreds of samples).
Use when after completing Cardinal-based preprocessing (feature summarization, TIC normalization, peak processing, spatial segmentation, and SSC annotation), use this conversion…
Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra)…
Use when you have positive- or negative-mode tunemix reference data (with known CCS values, m/z, and measured drift times) and need to establish a calibration model for converting…
Use when working with natural product molecules where conventional synthetic-molecule
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 after generating a count matrix from fragment data using pp.add_tile_matrix, pp.make_peak_matrix, or pp.make_gene_matrix in SnapATAC2.
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 you have a txt or tabular export file from a liquid chromatography–mass
Use when after drift correction and quality flagging, when you have a feature abundance matrix with associated metadata (Feature_ID, m/z, retention time) and need to identify…
Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
Use when after running fgsea() on a preranked gene list when you need to: (1) identify which pathways are most significantly enriched or depleted (lowest p-values), (2)…
Use when when loading MS/MS spectra from MGF files for FIDDLE model training or evaluation, or when preparing spectrum–annotation pairs for rescore model data augmentation (TCN…
Use when after labeling a representative subset of peaks (typically 10–20 pooled samples with corresponding feature tables) and before neural network training, when you need to…
Use when you have molecular descriptors or fingerprints for a set of compounds (e.g., from LC-MS metabolomics) and need to predict a continuous property—such as HPLC retention…
Use when after running omu_summary (t-test) or omu_anova (ANOVA) on metabolomics
Use when you have a trained PS2MS deep learning model, a set of evaluation compounds (especially novel NPS analogues), and want to understand whether prediction confidence…
Use when after running Enrichment() on a configured EnrichParam object (via KEGG_Enrich_PlotPanel or similar), when you have a full enrichment result table and need to reduce it…
Use when when deploying a Streamlit workflow app in offline mode (online_deployment:
Use when after loading a specXplore session data object file from the hard drive and instantiating a dashboard session layer with it, validate that the architecture layer has…
Use when when you have a tagged tabular file (Excel or CSV) with columns marked using export tag syntax (e.g., #study.id, #subject.id, #.
Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
Use when training a CNN model from scratch on LCMS peak classification tasks (or similar image-like batched data) where you need to confirm the model reaches target performance…
Use when you have per-feature CV values from quality control analysis of NMR or MS metabolomic data and need to: (1) establish whether your dataset meets FDA reproducibility…
Use when when you have raw mass spectrometry data from direct-infusion (DI-MS) or ambient surface analysis probe (ASAP-MS) instruments and need to identify which m/z peaks are…
Use when when a Shiny application is documented or observed to run only on Windows, blocking deployment to Linux or macOS users.
Use when you have raw UPLC-HRMS data from ThermoFisher or Agilent instruments and need to feed it into MSThunder for nontargeted pollutant identification.
Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).
Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain — from…
Use when you have sampled feasible flux distributions from multiple constraint-based
Use when building a metadata enrichment system that must support multiple pluggable converter backends and you need to automatically discover all available converters at runtime,…
Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format that have been converted to low-dimensional vectors via feature hashing, and you need to identify which…
Use when after completing the MS2LDA LDA modeling step when you have a JSON-serialized inferred motifset (Mass2Motifs with fragment and neutral-loss patterns) and need to annotate…
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 when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
Use when you have peptide sequences with chemical modifications encoded in ProForma notation (e.g., '[Phospho]-PEPTIDE[Carbamidomethyl]-C') and need to validate their syntax,…
Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf,…
Use when when preparing to read Thermo Fisher Scientific .raw files using rawrr functions (readFileHeader, readSpectrum, readChromatogram, readIndex), or when retrieving cached…
Use when apply CLR transformation when you have microbiome or metabolomic count data that sums to a constant across samples (relative abundance or compositional data) and intend…
Use when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical artifacts (batch…
Use when after importing MSI data as an msimat object and having a list of detected peak masses, but before annotating which mass differences correspond to biologically plausible…
Use when when you have raw mzML files and a feature table (CSV from mzMine or XCMS) with labeled peaks of unequal class sizes (e.g., fewer false positives than true positives) and…
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 you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to…
Use when when working with imaging mass spectrometry (IMS) datasets where you need to extract latent low-dimensional peak features from high-dimensional peak intensity data while…
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 you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction…
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 computed or received a precomputed expected contact frequency table (e.
Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures…
Use when after PCA dimensionality reduction and scaling of normalized, log-transformed gene expression data, when you need to identify local cell neighborhoods (typically with…
Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays
Use when you have raw GC-MS output in CSV format with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.
Use when you have centroid mzML files from LC-MS experiments (converted from Thermo .raw or other vendor formats) and need to identify and quantify individual chemical features…
Use when you have extracted retention times from top MS1 features in an LC-MS/MS experiment and need to assess whether the gradient configuration (start and end time in minutes)…
Use when when analyzing untargeted LC/HRMS data from population-scale projects (n > 500) spanning multiple sample batches or instrument runs, peaks with identical or…
Use when you have centroided mzML or mzXML LC-MS files from a single batch run that exhibit systematic retention-time drift between samples, one or more designated QC reference…