Use when you have raw SMILES strings from multiple external database sources (e.g., PubChem, ChEMBL, vendor databases) that need to be integrated into a unified structure…
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 you have downloaded raw LC-MS spectral peak data from a public repository (e.g., DOI 10.25345/C5FD2F) and need to ingest it into memory and prepare it in the format…
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 when you have .mzML or .abf LC-HRMS raw data files that require MS-DIAL-based feature detection, chromatogram alignment, and metabolite identification, and you need to…
Use when you have raw GC-MS data (aroma, breath, or other volatile analyte samples) in NetCDF or vendor-native format and need to identify multivariate chemo-/biomarker features…
Use when when you have trained a predictive model (e.g., neural network or regression model) that outputs continuous scores (such as Spearman correlation coefficients) for…
Use when you have raw MS intensity data paired with measurements from known concentration standards, and you need to produce absolute quantified concentration values rather than…
Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing…
Use when after mass-to-charge matching has produced a large table of candidate KEGG metabolites with multiple adduct assignments per feature.
Use when your XCMS-processed LC-MS dataset exhibits retention-time drift or misalignment artifacts—particularly when analyzing hundreds of samples, data acquisition spans longer…
Use when when annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches…
Use when you have processed MSI peak data (in rMSIproc format) and need to distinguish matrix-related ions from analyte signals.
Use when you have (1) genomic data from a Streptomyces or other RiPP-producing organism in raw FASTA format or annotated GenBank format, (2) high-resolution LC-MS/MS spectra in…
Use when you have a single-cell count matrix with 10 million or more cells that must be processed through dimension reduction, clustering, or integration pipelines.
Use when you have measured CCS values from (LC-)IM-MS samples spiked with U¹³C labeled internal standards (e.
Use when when running metabologenomic RiPP detection pipelines (MetaMiner) on the same genomic dataset but with different input sequence formats (e.g., contigs.fasta vs.
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 you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or…
Use when after constructing a network graph where nodes represent Mass2Motifs (or spectra) and edges encode pairwise spectral similarity scores, and you need to export the network…
Use when when you have a processed or annotated MsmsSpectrum object (from USI loading or direct instantiation) and need to generate a figure showing observed peaks, their…
Use when you have imported a raw LA-ICP-MS raster image (line-by-line, spot-wise, or ablation-time-aligned format) and need to isolate tissue regions from instrumental background…
Use when after peak picking and alignment have been performed on MSImagingArrays
Use when after standardizing link scores (strain correlation and IOKR) across all potential GCF-MF pairs in a metabologenomics dataset, perform significance testing to determine…
Use when you have imaging mass spectrometry (IMS) datasets with peak intensity features organized as spatial graphs (nodes = pixels/voxels, edges = spatial adjacency), and you…
Use when you have located a workflow definition file (YAML or JSON) from a versioned release and need to confirm that all mandatory workflow metadata fields (name, version,…
Use when you have a trained baseline GNN model with established hyperparameters (dropout rate, learning rate, epochs, optimizer settings) and want to evaluate whether alternative…
Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library…
Use when after XCMS peak picking and fillPeaks() when you have xcmsEIC and filled xcmsSet objects and need to systematically flag low-quality or unreliable peak integrations prior…
Use when you receive a JSON response from a REST API endpoint (e.g., TensorFlow Serving /model/metadata) and need to extract and validate specific fields such as model input…
Use when after generating or filtering transformation products using generateTPs() or filter(), when you need to annotate MS/MS spectra using MetFrag and require a database of…
Use when you have intracellular metabolomics concentration measurements across multiple cell lines or conditions, a stoichiometric metabolic network model with reaction-metabolite…
Use when configuring a new injection-plate design template in InjectionDesign if you have multiple QC types to position on a plate and need to visually distinguish them in the…
Use when before running any R function that wraps compiled C# methods or system executables (e.g., rawrr::readSpectrum), especially when the package depends on language runtimes…
Use when your input is an AnnData object with expression matrix X as a sparse scipy matrix or Dask-backed array, and you need to apply preprocessing functions (normalization, PCA,…
Use when you have obtained MobiLipid or a similar IM-MS lipidomics package that bundles a CCS reference library for labeled lipids, and you need to verify library integrity,…
Use when you have a GNPS-generated molecular network (graphml or JSON format) and corresponding MS2LDA experiment results or chemical class assignments, and you want to annotate…
Use when you have raw or folded 2D-TIC chromatogram data (typically imported from NetCDF files into RGCxGC chromatogram objects) that exhibits baseline drift, chemical noise, or…
Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained…
Use when when you need to establish a working installation of a Python package in a fresh or isolated environment, particularly when the package is available through multiple…
Use when after applying batch correction (e.g., via pycombat) to a multi-batch feature table, to validate whether the correction has reduced systematic intensity differences…
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 raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z…
Use when you have raw spectroscopic datasets from heterogeneous sources (multiple Zenodo repositories with different file formats and scales) that must be jointly normalized,…
Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.
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 mzML mass spectrometry files that need both compression and rapid random access by spectrum ID (e.g., direct retrieval of spectrum 2540 without sequential…
Use when after creating a methylRawListDB object via methRead() with dbtype='tabix', or when loading pre-existing tabix-backed methylation files, to verify that bgzipped files are…
Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform…
Use when you have a raw NV (NMRViewJ) binary file and need to confirm it is well-formed before parsing or processing.
Use when when you have a large collection of reference MS/MS spectra (spectral library) and need to search unknown query spectra against it rapidly, particularly for open…
Use when after peak detection when you have a table of detected peaks with m/z values and need to improve mass accuracy for downstream annotation.
Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
Use when you have a tandem mass spectrum with observed m/z peaks and a known peptide sequence (as a ProForma string, optionally with post-translational modifications), and you…
Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible
Use when when designing or integrating a file parser for mass spectrometry formats (.raw Thermo RAW format, .mzml XML-based format) in a metabolomics processing pipeline, or when…
Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment…
Use when you have a SummarizedExperiment object containing NMR or MS metabolomic data with aligned phenotype information (BMI, disease status, age, gender), and you need to…
Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments,…
Use when after training multi-layer perceptron neural networks via cross-validation