Use when you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass…
Use when when you have Spectra objects in R and need to apply Python MS library functionality (spectral similarity scoring, filtering, normalization) without leaving the R…
Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a…
Use when after peak picking across individual spectra in an MSImagingExperiment,
Use when you have a collection of preprocessed tandem mass spectra (binned into 10,000 equally-sized m/z bins, intensities square-root transformed, top 1,000 peaks retained), a…
Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL…
Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with…
Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign…
Use when you have raw or processed mass spectrometry data in HDF5 (.h5) or mzML format and need to ingest it into DEIMoS for multi-dimensional analysis.
Use when designing or validating a metabolomics pathway analysis experiment, especially when you have uncertainty about how many metabolites your detection platform will reliably…
Use when when performing targeted quantification of known compounds in LC-MS data using TARDIS, especially when the instrument acquired data with multiple overlapping m/z scan…
Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
Use when you have MS-DIAL lipid identification results (alignment exports in msp/txt format) and need to distinguish correct from incorrect lipid IDs before downstream analysis.
Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context…
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 when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each…
Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and…
Use when after calling squidpy.gr.spatial_neighbors or any graph-building operation that outputs sparse matrices to adata.
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…
Use when you have extracted a centroided MS/MS spectrum from a Thermo Orbitrap raw file (via rawrr::readSpectrum or equivalent) and need to verify that the observed y-ion…
Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity,…
Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to ident — from…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute stable variance estimates and differential expression sta — from…
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 you have raw metabolomics data files in one or more of the supported formats (.raw from Thermo instruments, .d directories from Agilent, or mzXML open-format exports) and…
Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization…
Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique…
Use when when you have extracted and concatenated MS/MS spectra from multiple replicates for a set of metabolomic features (stored in a preprocessed list), and need to apply…
Use when you need to run the Zamboni-lab Masster (MASSter) workflow for untargeted LC-MS metabolomics data analysis.
Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and…
Use when you have one or more MS/MS query spectra (in mzML, mgf, msp, mzxml, json, or pickled matchms format) and a pre-built spectral library stored in SQLite with precomputed…
Use when you have two implementations of the same quantification method (or major versions) and observe a persistent disagreement in mapped-read counts, per-read alignment…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the n — from…
Use when when you have access to a research repository or README documenting a machine learning implementation (e.g., Keras/TensorFlow-based deep learning model) and need to…
Use when when you have experimental MS/MS data (peak lists, precursor m/z, charge state, adduct type) paired with a chemical structure (SMILES or structural identifier), and need…
Use when you have selected statistically significant features from multi-assay untargeted LC-MS metabolomics data and need to group them by structural relationships defined by…
Use when you have paired in silico and experimental measurements from multiple biological samples (e.
Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular…
Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples…
Use when you need to validate that a software project''s release branch is stable and ready for distribution.
Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
Use when you need to open an mzML file in pymzML and must automatically select the correct handler based on file extension (.mzML, .mzML.gz, .db) and—for gzip files—indexed vs.
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 a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or…
Use when you have transcript abundance estimates from RNA-seq quantification tools (e.
Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or…
Use when when you have raw or GNPS-processed MS2 spectral data from microbial strains and need to organize spectra into molecular families (grouped by spectral similarity) while…
Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference…
Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.
Use when you have loaded processed LC-MS data (mzML or vendor format) and need to establish baseline instrument performance before evaluating sample analytes.
Use when you need to obtain source code or computational workflows from a published repository, particularly when the article explicitly provides a GitHub URL and documents that…
Use when after running spectral networking on tandem MS data and obtaining a network graph, when you need to assess which spectra cluster together, determine cluster…
Use when when you have a feature intensity table (samples × compounds) from targeted or non-targeted metabolomics and need to prepare it for statistical modeling or multivariate…
Use when when a QC check fails during an LC-MS instrument run and you need to alert users in real time.
Use when you have LC-MS/MS data acquired in DDA mode from untargeted metabolomics experiments and need to remove chimeric (co-fragmented) MS/MS spectra that result from multiple…
Use when when you have raw or lightly processed 1D NMR spectra (¹H and/or ¹³C) from unknown organic compounds and need to extract latent spectral features prior to structure…
Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the…
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 when you have raw count matrices from paired microbiome (16S rRNA or metagenomic) and metabolomic (LC-MS/MS) profiling data that will be used to train or apply a…