Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic…
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 fitted alignment model (e.g., metabCombiner object with pre-aligned feature pair candidates and RT spline mapping) and known shared compound identities (ground…
Use when you have a detected LC-MS feature table (with m/z, retention time, and intensity columns) and need to identify which features are derivatives of the same parent molecule…
Use when you have deconvoluted or processed MS/MS spectra from SWATH-MS data that need to be (1) ingested into tools requiring open formats (e.g., spectral library matching,…
Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time…
Use when after calling buildExperiment on metabolomics data to construct a SummarizedExperiment object, before performing batch correction, outlier detection, or other QC…
Use when you have precomputed expected contact frequency tables (TSV format with columns like dist_bp, contact_frequency, n_valid) and need to apply log-binning and smoothing to…
Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when…
Use when after feature detection has produced a feature table with zero and missing values (sparse abundance matrix) but before multivariate statistical analysis or annotation.
Use when you have an enumerated list of lipid species (identified by class, fatty acid composition, and chain length) and need to generate theoretical precursor m/z values,…
Use when when you have paired spatial transcriptome and metabolome datasets in h5ad format with spatial coordinate matrices (obsm['spatial']) and you need to establish spot-level…
Use when when you have loaded centroided .mzML files into a Spectra object and plan to use TARDIS (tardisPeaks) with an MsExperiment object rather than file paths, and you need…
Use when you have transcript-level quantification files (quant.gz, h5, or similar) from a known upstream quantifier (salmon, kallisto, sailfish, oarfish) and need to import them…
Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible
Use when when you are developing or contributing to a Python package (like cooltools) and need to test changes to utility functions, library integrations, or API implementations…
Use when you have acquired high-resolution MS/MS spectra in mzML, mzXML, or MGF format and need to prepare them for large-scale clustering or similarity searching.
Use when when you have constructed a MassGrid (m/z-aligned mass tracks across multiple samples) and need to retrieve all sample-specific mass tracks for a given m/z value in order…
Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
Use when after identifying statistically significant features and assigning them to structural clusters (isotopologue groups, adduct groups, cross-assay links) and correlation…
Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by…
Use when when you need to verify whether a specific mass spectrometry instrument platform (vendor and model), acquisition mode (e.g., targeted, ddMS2-topN, AIF, direct infusion,…
Use when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each…
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 you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass…
Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and…
Use when you have completed DESeq differential expression analysis on a DESeqDataSet and obtained raw results with p-values across all genes.
Use when you need to quantify the degree of match between two MS/MS spectra—either
Use when you have predicted retention times from one or more machine learning models (DNN, Gaussian Process, or ensemble) applied to small-molecule chromatography data, along with…
Use when when you have high-dimensional replicate experimental data (e.g., metabolomics, proteomics, genomics assays) where technical or biological variability threatens…
Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type…
Use when when you have access to the MAGMa source code and need to understand or audit how in silico metabolite candidates are enumerated from parent structures.
Use when you have LC-HRMS profile-mode chromatograms with extracted local maxima exported as standardized 2D rt×mz areas, and you need to disambiguate true chromatographic peaks…
Use when you have selected a subset of ReDU public tandem MS files with GNPS chemical annotations (level 2 or 3 spectral library matches) and wish to explore sample relationships…
Use when you have two or more CSV feature tables from independent metabolomic experiments (each with RT, m/z, intensity, isotope, and adduct columns), and you need to merge them…
Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
Use when when you have a Thermo Fisher Scientific Orbitrap .raw file and need to confirm that a targeted acquisition method (e.g., PRM targeting a specific precursor m/z) is…
Use when you have a published scientific article describing a computational method (e.g., natural products annotation, MS/MS data processing) and need to assess reproducibility…
Use when you are starting a new mass spectrometry analysis task or feature request where the problem scope is unclear, the tool chain (e.g., OpenMS + Python + KNIME integration)…
Use when you have a compiled EI or MS2 library object (read from MSP format via read_lib) and access to NIST ri.dat and USER.DBU files; you need to populate RI values for…
Use when after applying CordBat batch correction to a log2-transformed metabolite matrix from multi-batch metabolomics data, you want to quantitatively and visually assess whether…
Use when you have multiple LC-MS runs with the same set of targets (compounds) and observe or expect retention time drift or jitter between runs.
Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before…
Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit…
Use when you have measured execution times from multiple scripts that exercise different combinations of categorical variables (e.g., plot types: chromatogram, mobilogram,…
Use when you have adapter-trimmed FASTQ files and need to obtain transcript-level
Use when you have raw MS data files in vendor-native format (.raw, .d, .ms) from CE-MS or LC-MS instruments and need to process them through AriumMS or other open-source…
Use when you have uploaded a pre-analytical data table containing sample metadata, processing timestamps (pre- and post-centrifugation), and NMR metabolomic measurements — from…
Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's…
Use when you have generated hypothetical links (e.g., GCF–MF pairs) and computed multiple independent scoring functions on them (e.g., strain co-occurrence, IOKR structural…
Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect…
Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench
Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by…
Use when you have large spectral libraries (thousands to millions of spectra) and need to search query spectra against them for peptide identification with tolerance for…
Use when you have molecular structures (SMILES or SDF format) for which you need to predict retention time in liquid chromatography, especially when your target dataset contains…
Use when your spatial metabolomics dataset contains raw m/z features (e.g., from MALDI-MS imaging or LC-MS/MS) without metabolite annotations, and you have selected a reference…
Use when you have a Chemical Feature Tree artifact (phylogeny) output from q2-qemistree's make-hierarchy method and need to verify its structural validity, count nodes (leaves and…
Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run…
Use when when you have applied multiple scoring functions (e.g., strain correlation and IOKR) to rank genomic-metabolomic (GCF-MF or BGC-spectrum) links and need to verify that:…