Use when you have a chromVARDeviations object with precomputed bias-corrected deviations and z-scores for multiple annotation sets (e.
Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.
Use when after computing aggregate statistics (mean, median, standard deviation, frequency distributions, similarity coefficients) over a large dataset of molecular fingerprints…
Use when when searching unknown mass spectra against large high-resolution spectral libraries for open modification identification and you need to reduce search latency from…
Use when when you have cloned or accessed the Reverse_metabolomics_library_generation
Use when after sending HTTP requests to API endpoints (such as /classify or /model/metadata on an NP-Classifier server) to verify that the response is parseable JSON and contains…
Use when when you have mass-spectrometry data (m/z and intensity pairs or spectral matrices) paired with ground-truth molecular fingerprints or InChIKeys, and you need to learn a…
Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data…
Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for…
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 when you have metabolite structures (as SMILES strings) and need to predict their observable m/z ions under non-standard ionization conditions imposed by a derivatizing…
Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
Use when when you have published LOTUS flat files (TSV or compressed TSV.GZ) containing structure-organism pairs and need to enumerate unique structures, group by organism…
Use when when you have a resolved spectrum file in mzML or mzXML format and need to identify where MS2 (tandem mass spectrometry) scans occur within an LC-MS run, particularly to…
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 preprocessed MSI data (as a CSV intensity matrix or Cardinal MSProcessedImagingExperiment object) and suspect that observed peaks include both parent ions and…
Use when you have a set of preprocessed MS/MS spectra (binned to 10,000 m/z bins with intensities square-root transformed) and a trained MS2DeepScore Siamese neural network model,…
Use when after peak quality filtering has been applied to a composite map peak detection output using SNR (>2), goodness-of-fit (peakshape > 0.5), minimum peak height (default…
Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or…
Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
Use when after applying cluster-based filtering with quasi-molecular adduct constraints and frequency thresholds on LC-MS feature candidates, when some peaks have been entirely…
Use when you have a collection of pre-processed MS/MS spectra (binned, intensity-normalized) and a trained MS2DeepScore base network, and you need to compute structural similarity…
Use when when you have mass spectrometry raw data (DI-MS or ASAP-MS format) from plant samples that are easily confused due to morphological similarity, or when you need to verify…
Use when when XCMS-aligned LC-MS data shows coefficient of variation (CV) above expected thresholds for known features, or when analyzing long-duration experiments (>1 week) or…
Use when you have mass spectrometry data available in multiple identifier formats (GNPS Task ID, Universal Spectrum Identifier, or Feature-Based Molecular Networking task…
Use when you have CE-MS raw data in OnDiskMSnExp format with both positive and negative polarity acquisitions, migration times that vary due to electroosmotic flow drift, and…
Use when when you have applied biotransformation rules to generate candidate product structures from a set of input molecules (represented as SMILES strings) and need to document…
Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single — from…
Use when you have aligned feature tables (CSV format) paired with MS2 spectral data (MGF or mzML files) and need to compare chemodiverse samples with poor feature overlap or…
Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a…
Use when when performing ChIP-Seq peak calling with MACS3, after duplicate filtering and fragment length prediction (d), to construct the background model that will be compared…
Use when executing containerized conversion tools (e.g., AirdPro CLI) that must read vendor-format mass spectrometry raw files from the host filesystem and write converted output…
Use when when you have computed similarity scores (cosine, modified cosine, Spec2Vec, or other metrics) between a set of query spectra and a reference library with known…
Use when you have raw LC-HRMS profile-mode data and need to identify candidate chromatographic peaks before classification or feature extraction.
Use when you have a defined set of lipid species (identified by class and fatty acid composition) and need to create a high-throughput spectral library for mass spectrometry-based…
Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request.
Use when after completing multidimensional smoothing and saturation repair on Agilent MassHunter (.
Use when you have MGF or native MS/MS arrays (mz_array, intensity_array, precursor_mz, adduct) and want to predict the most likely molecular formula.
Use when when you have a set of molecules with known chemical structures and need to prepare them for classification or prediction tasks.
Use when when you have paired spatial transcriptome and metabolome datasets with spot-based coordinates that need to be aligned for multi-modal integration.
Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
Use when you have a Sciex Multiquant TXT export file containing a metabolomics or lipidomics analytical sequence and need to locate QCpool samples that were injected at regular…
Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that…
Use when you have raw mass spectrometry spectra (in MGF, mzML, or similar formats) that must undergo standardized preprocessing before library matching, similarity searching, or…
Use when after XCMS feature detection and alignment when you have a CSV-formatted
Use when you have RNA-seq read count data and a metabolic model with GPR rules, and you need to assess how differential gene expression translates into differential metabolic…
Use when you have at least 3 raw mass spectrometry samples in open formats (mzML, mzXML, CDF) from untargeted metabolomics experiments and need to configure parameters for XCMS,…
Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT.
Use when when you need to understand the modular composition of a multi-component research software project, particularly before onboarding, refactoring, or deploying it.
Use when you have processed MSI data (peak matrix and spatial coordinates) from matrix-assisted laser desorption/ionization (MALDI) or silver-assisted laser desorption/ionization…
Use when working with raw or minimally processed MS/MS spectra from repositories
Use when when fitting a nonlinear retention time (RT) mapping spline to anchor feature pairs (m/z and RT values) from two LC-MS datasets acquired under different conditions, you…
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 you have a C# GUI application targeting .NET Framework 4.8 (Windows-only)
Use when after a deep neural network model has completed training on LC-MS spectral peak classification data and you need to preserve the learned weights and architecture for…
Use when you have LC-IM-MS/MS raw data from multiple tissue samples and need to identify and quantify unsaturated sterol lipids at the isomer level (distinguishing double-bond…
Use when you have MS/MS spectra contaminated with chemical noise (spurious fragment ions that do not correspond to real chemical bonds or rearrangements), a known or predicted…
Use when when you have processed scATAC-seq data (peak calling complete, cell-barcode matrix generated) and need to register it into ArchR for downstream multiome analysis…
Use when you have a pre-computed hierarchical dendrogram from correlation-based clustering of LC-MS features (with fixed linkage criterion and distance metric) and need to decide…