Use when after matching mass-to-charge ratios to a compound database (e.g., KEGG) and assigning adduct/fragment types, when you have an annotated feature table with retention…
Use when when you have a preprocessed bag-of-fragments corpus from tandem mass spectrometry spectra and need to train an MS2LDA model to discover Mass2Motifs.
Use when you have a trained NeatMS neural network model (.h5 format) and need to assess its classification performance at a specific decision threshold (e.g., 0.01) to de — from…
Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
Use when immediately after extracting ion chromatograms (EICs) by binning mass spectral data across the full m/z range from raw LC/HRMS files (mzML, mzXML, or netCDF format).
Use when when processing low-resolution GC-MS data in NetCDF format where you have already performed retention-index calibration and peak deconvolution, and you need to assign…
Use when when an algorithm claims linear or sublinear time/space complexity (e.g., matrix-free spectral embedding) and you need to verify that claim holds for datasets at the…
Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against…
Use when when you have RNA-seq count matrices (from HTSeq, featureCounts, Salmon, kallisto, or RSEM quantification) and need to test for differential expression between two or…
Use when you have acquired one or more tandem MS/MS spectra and need to identify metabolites against a reference library filtered by biological domain (e.
Use when after converting proprietary vendor mass spectrometry files (Thermo .raw, Agilent .d, Bruker .d, or mzML) to MZA HDF5 format using the MZA executable.
Use when you have computed raw strain correlation scores and IOKR scores for the same set of GCF–MF (gene cluster family–molecular feature) pairs, and you want to compare or…
Use when you have executed mzExacto() on a preprocessed GC-MS dataset and need to verify that the returned dataframe correctly matches query chemicals to their m/z peaks,…
Use when you need to add a new local chemical structure conversion capability to MSMetaEnhancer when existing web-service converters (CTS, CIR, PubChem) are unavailable, too slow,…
Use when you have a Thermo Fisher Orbitrap .raw file and need to programmatically
Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for…
Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both…
Use when you have a known compound structure with validated MS/MS spectrum and a structural analog (modified version) with its own MS/MS spectrum, and you need to assess whether a…
Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage,…
Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate, octanal, undecane) and need to evaluate them against reference compound categor — from…
Use when when training or validating a deep learning model for molecular formula prediction from tandem MS/MS spectra, use this metric to track whether the model's predicted…
Use when after computing a scoring function over all possible genomic-metabolomic candidate pairs (e.g., all 2966 MIBiG-GNPS BGC-spectrum pairs), when you have a subset of known…
Use when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical artifacts (batch…
Use when you have raw mass spectrometry data in mzML or Bruker .d format and need to ingest it into a tabular format (pandas DataFrame) for visualization, statistical analysis, or…
Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to…
Use when after mass tracks have been aligned across all samples into a MassGrid (via sample-wise or centroid-based alignment), you have a unified set of m/z features tracked…
Use when when you have parallel mass spectra and molecular structure data (e.g., CANOPUS or MassSpecGym datasets) and aim to train a single encoder-decoder model (e.g., BART) that…
Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among…
Use when you have a combined EI library (from multiple sources such as NIST, RIKEN, MoNA) and access to NIST RI database files (ri.dat and USER.
Use when after acquiring MS/MS spectral data from untargeted metabolomics experiments and having candidate transformed structures from biotransformation rule application.
Use when after extracting tabular data into intermediate JSON representation (via tagging), or after manual JSON editing, and before converting to a target format (e.g., mwTab for…
Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original…
Use when you have validated intermediate JSON data (conforming to the Experiment Description Specification) and need to configure how it should be converted to a supported output…
Use when after peak picking has generated a peaklist of experimental fragment m/z values (from Q-Exactive orbitrap, Agilent/Bruker/SCIEX Q-TOF UHPLC-HRMS/MS, or direct…
Use when you have a connected subnetwork of LC-MS features that matched isotope or adduct patterns, and you need to establish a canonical tree representation with a single neutral…
Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a…
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 after mass tracks have been aligned across all samples (either via pairwise alignment for ≤10 samples or nearest-neighbor clustering for larger cohorts), and you need to…
Use when you have a set of chemical compounds (with known retention times and intensities) loaded into a ViMMS IndependentMassSpectrometer and need to simulate a specific MS/MS…
Use when apply PCA when you have a log-normalized, scaled gene expression matrix from highly variable genes and need to reduce dimensionality before constructing k-nearest…
Use when after MS-Dial peak picking and feature table construction, when you observe a high proportion of features with anomalous m/z decimal values that are inconsistent with…
Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and…
Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to synthesize results across domains (e.
Use when after mass track construction for individual samples, when you need to establish consensus m/z values across a cohort of LC-MS samples to build a unified feature table.
Use when when you have a set of chemical structures (SMILES strings or SDF files) that need to be processed for training a graph neural network model on molecular property…
Use when after running XCMS-based alignment on LC-MS datasets with hundreds of samples or data acquisition periods longer than a week, when the assumption that all m/z bins in the…
Use when converting JSON metadata and you need to populate a target field by selecting or iterating over records only when they satisfy a logical test condition (e.g., 'include…
Use when you have a set of candidate metabolites for an unknown compound detected in a liquid chromatography–mass spectrometry (LC-MS) experiment, predicted RTs from a trained DNN…
Use when when implementing a custom MsBackend and the spectraData() method needs to return all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of…
Use when when you have MS/MS fragment spectra (in .mgf format) acquired from unknown metabolite features and need to annotate them against known compounds.
Use when after batch correction of metabolomics data using pooled study quality control (SQC) samples and calculation of compound/internal standard ratios, when you need to decide…
Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
Use when when you have preprocessed MS/MS spectral data (filtered, noise-reduced,
Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction.
Use when when you have salmon quant.sf.gz output files from pseudoalignment-based transcript quantification and need to convert transcript-level abundance estimates and counts…
Use when you have xcms-processed LC-MS data with detected misaligned feature groups and need to recover the underlying raw retention time–intensity profiles for each feature and…
Use when when processing open mass spectrometry library (OMSL) data that may contain duplicate spectral records (e.
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 CDF-format mass spectrometry imaging files from plant roots with accompanying MATLAB workspace files (.mat), and your research goal is to reproduce linear-axis…