Use when after serializing empirical compound collections to JSON format via khipu's build_empCpds command, or before ingesting empCpd.
Use when you have a feature table from LC-MS data alongside blank (solvent-only) sample runs, and you want to remove features whose intensity in study samples is not substantially…
Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate) and need to find their -matched structural analogues within a reference library — from…
Use when when you have raw tandem mass spectrometry peak data (m/z and intensity pairs), precursor m/z, charge state, and adduct annotation for one or more compounds, and need to…
Use when when converting MS/MS spectra from .msp format library files (e.g., MassBank) into a custom fragment library for metabolite annotation, and the source spectra are tagged…
Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES),…
Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected…
Use when you have PSI (percent-spliced-in) matrices for multiple samples grouped into two or more biological conditions, along with corresponding transcript expression…
Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before…
Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts…
Use when you have a normalized gene expression matrix (genes × samples) and an experimental design with known treatment groups or conditions, and you need to estimate the effect…
Use when you have a compressed file format (e.g., igzip) with a custom binary header structure that encodes metadata (index-to-offset mappings) in a fixed layout, and you need to…
Use when when you have trained multi-layer perceptron neural network models on paired microbiome-metabolome data (from ≥10-fold cross-validation iterations) and need to identify…
Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign…
Use when when you have a tandem mass spectrometry spectrum with a known or inferred peptide sequence that may contain post-translational modifications (phosphorylation,…
Use when when you have transcript-level quantification files (e.g., Salmon quant.sf.gz, kallisto abundance.h5, or RSEM .results) and need to construct a gene-level count matrix…
Use when you are preparing to perform effective mobility transformation of CE-MS data and must establish the electrophoretic system's calibration context.
Use when you have a set of natural product molecules (or suspected natural products) in SMILES, InChI, or SDF format and need a chemical representation suitable for biosynthetic…
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 you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment.
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 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 aligned feature table from untargeted LC-MS with missing intensity values (NA or zero entries) for features that are present in some samples but fell below…
Use when a mature scientific package (e.g., Mummichog 3) is being migrated to a new GitHub organization that enforces standardized project structure, and the current setup.py,…
Use when you have trained multiple machine learning classifiers (e.g., AdaBoost, SVM, Random Forest) on the same metabolomics peak-quality training set using k-fold…
Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to…
Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that…
Use when you have structural input data (SMILES or molecular geometry files) for N-Me derived unsaturated sterol lipids and need to generate a predicted CCS dataset indexed by…
Use when you have an untargeted metabolomics feature table (m/z values, retention times, p-values from statistical testing) and need to infer which metabolic pathways are active…
Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C-labeled yeast extract, measured CCS values for both labeled and unlabeled lipids, and need to quantify…
Use when you have a large gene expression matrix (e.g., thousands of genes) from normalized microarray or RNA-seq data and need to reduce computational burden before running…
Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you need to link individual m/z features into structural clusters represent — from…
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 when implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
Use when you have an untargeted metabolomics feature table with m/z values, retention times, intensity measurements, and p-values from statistical testing, but lack or wi — from…
Use when you have a Thermo Orbitrap .raw file and need to (1) verify that a targeted acquisition method (e.g., PRM) maintains consistent scan spacing across all cycles; (2)…
Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar…
Use when when searching for peptide spectra with unknown or open modifications (i.e., any mass shift within a broad tolerance range rather than a fixed set of known modifications).
Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the…
Use when you have received MSBERT-preprocessed spectral data from GNPS, MoNA, or MTBLS1572 and need to ensure data integrity before training a spectral embedding model.
Use when you have observed mapping rate or quantification disagreement (e.g., >0.1% divergence in mapping rate or Pearson r < 0.
Use when after peak-picking stage completes on centroided mzML or netCDF raw LC-MS data via any of the three wrapped algorithms (Centwave, FeatureFinderMetabo, ADAP), when you…
Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.
Use when after mass-difference network generation has matched pairwise peak mass differences to a reference biochemical transformation key with mass error ≤1 ppm, and you need to…
Use when you have a GC-MS dataset with Match.Factor scores for each detected compound (output from Agilent Unknowns Analysis or equivalent), and you want to reduce the number of…
Use when after generating large feasible flux distributions (e.g., 1 million sampled solutions per cell line) from constrained metabolic models, apply t-SNE when you need to…
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 you need to understand how a complex MS/MS spectral search system routes query spectra through multiple parallel processing pipelines with different objectives (e.g.,…
Use when when you have authored a custom .csv lipid library and need to confirm it adheres to LipidMatch's documented schema before placing it in the designated library directory…
Use when when you need to generate reproducible synthetic LC/GC-MS raw data files with known ground-truth peak properties (m/z, retention time, intensity) for benchmarking peak…
Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators)…
Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes…
Use when after initial retention-time-based feature grouping (e.g., ±20 s window) when you need to separate co-eluting features that are chemically distinct.
Use when you have split multi-assay LC-MS intensity data into training (90%) and test (10%) subsets with assay-specific column prefixes, and you need to fit a discriminant or…
Use when after mass track extraction and alignment across samples, when you have a MassGrid structure (m/z-aligned mass tracks) and corresponding retention time calibration…
Use when you need to validate batch correction or normalization algorithms, require ground-truth condition/batch effect annotations for method benchmarking, or want to…
Use when you have paired predicted and observed metabolite abundance vectors from a predictive model (e.
Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full…