Use when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict which fragments will appear with high intensity in a tandem MS spectrum, or when…
Use when you have raw tandem mass spectra data (mz/intensity pairs and precursor m/z values) and need to train interpretable machine learning models (regression or tree-based)…
Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign…
Use when after applying AbundanceSimilarityParam (with threshold ≥0.7 and log2 transform) to retention-time-based feature groups from SimilarRtimeParam, when you need to examine…
Use when after running salmon quant with the --writeMappings/-z flag to produce SAM output, or when investigating discrepancies between the number of mapped reads reported in…
Use when you have raw or normalized single-cell RNA-seq expression data stored in an AnnData object (`.h5ad` format) and your analysis goal is to infer developmental or…
Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness,…
Use when you have a pre-trained DNN RT predictor (e.g., trained on METLIN SMRT with 80,038 experimental RTs) and need to adapt it to predict retention times in a new or external…
Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular…
Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal…
Use when when you have raw or processed TWIM-MS data (arrival time and m/z values) from a mass spectrometry instrument and need to organize it into a feature table before…
Use when after nontargeted peak detection has identified candidate peaks in LC-MS chromatograms, when you need to establish exact peak start/end retention times and extract…
Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
Use when you need to systematically enumerate all possible lipid species within a defined analytical scope—specifically when you have specified one or more lipid classes (e.g.,…
Use when when you have preprocessed mass spectrometry ion images (single-channel
Use when when you have tandem mass spectra from ribosomally synthesized peptides (RiPPs) and suspect the presence of unknown or non-standard post-translational modifications that…
Use when after peak detection and clustering have been completed on aligned and baseline-corrected GC-IMS data, and before imputation or statistical analysis.
Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
Use when you have one or more small-molecule chemical structures (as SMILES, MOL, or SDF) and need to systematically explore their fate across mammalian biotransformation, human…
Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and…
Use when after a machine learning model has generated predicted molecular structures (connectivity graphs and molecular formulas) from 1D NMR spectra.
Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments…
Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a…
Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or…
Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of…
Use when your m/z peak data spans multiple batches (recorded in metadata as a batch ID column) or samples have varying concentrations that are documented in metadata.
Use when you have preprocessed, normalized beta-value matrices from EPIC or 450k methylation arrays with at least two sample groups (case/control, treatment/untreated, or similar…
Use when you have raw LC-MS/MS data acquired in Data-Dependent Acquisition (DDA) mode and need to create a labeled training dataset for customized purification model development.
Use when you have a versioned workflow definition file (YAML or JSON) from a specific release commit and need to verify it conforms to the project's schema specification, validate…
Use when when comparing two preprocessed MS/MS spectra for compound identification
Use when after kNN imputation of metabolite measurements but before variance-stabilizing
Use when you have Sciex Multiquant txt exports containing signal intensities from QCpool samples injected at regular intervals (e.g., every 10–20 samples) during one or more…
Use when after running inference on test mass spectrometry spectra with a trained deep learning model (e.g., PS2MS) to verify that class label predictions and confidence scores…
Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and…
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 retrieved chemical formulae and metadata from two or more of HMDB, ChEMBL, or PubChem and need to merge them into a single searchable database without formula…
Use when after peak detection and feature extraction have produced a composite feature table with m/z, retention time, and intensity values for individual samples.
Use when when you have raw TWIM-MS arrival-time data and need to transform it into absolute CCS values for downstream biomolecular class assignment or comparative analysis.
Use when when running a ViMMS Environment simulation with save_eval flag enabled and you need to correlate fragmentation events in the output mzML file back to their originating…
Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for…
Use when after batch effect removal and sample integration, when you have a normalized feature-by-sample abundance matrix (finalData) with corresponding sample group labels…
Use when you have uploaded MS/MS data to MassIVE with validated sample-information
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 when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform…
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 you have LC-HRMS chromatograms in retention time × m/z matrix format and need to automatically localize chromatographic peak positions and extents prior to matching…
Use when you have a peak list extracted from MSI data that includes candidate peaks with potential m/z overlap or spatial co-localization patterns across tissue images.
Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate…
Use when you have MS/MS spectra matched to a reference library via both identity search (exact or high-similarity matches) and fuzzy/analog search (structurally related compounds…
Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.
Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural…
Use when you have GC–MS or LC–MS data represented as a two-dimensional map with m/z values on one axis and retention time on the other, and you need to identify analyte signals…
Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a…
Use when you have mass spectrometry data stored in a SQLite database indexed by spectrum ID and need to retrieve specific spectra by ID (random access via __getitem__) or iterate…
Use when you have a trained decision tree model on ChemEcho sparse feature vectors and need to convert a specific decision path (root to leaf) into a deployable query.
Use when when comparing quantification results between two versions of a tool (e.g., salmon 2.0 Rust rewrite vs.
Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be…
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…