Use when you have raw LC/MS data in mzML format and need to perform non-targeted
Use when after extracting raw MS/MS spectra from mzML files for individual features (identified by precursor m/z and retention time) and you have multiple replicate spectra for…
Use when input GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks where multiple analytes co-elute at the same retention time, resulting in composite…
Use when after anchor selection and retention-time spline mapping have produced a candidate list of feature pair alignments, but before final scoring and reduction of the combined…
Use when after identifying putative BGC-encoded precursor peptides from a genome assembly via MetaMiner's BGC identifier, when preparing a RiPP structure database for downstream…
Use when you have raw MS intensity tables showing systematic drift during a measurement sequence (e.g., declining or variable ion counts across a run), particularly in targeted…
Use when when processing sequential spectroscopic data (1H NMR spectra) where both local chemical shift patterns and global spectral dependencies are needed for compound…
Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or mzData format from LC-MS/MS analysis; (2) a set of predicted RiPP precursor peptides derived from genomic…
Use when after peak picking by MS-DIAL and import into R, when the feature table contains m/z values with decimal components that fall within the [4, 8] interval (indicating…
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 when constructing k-nearest neighbor graphs from spatial coordinates (e.g., microscopy x,y positions or tissue section coordinates) and exact neighbor discovery is…
Use when when you have a list of chemical compounds (with m/z values, retention times, and intensities) and need to simulate their acquisition behavior under a specific ionization…
Use when when you need to create negative control or background-only reference datasets for LC/GC-MS analysis pipelines—specifically to validate peak-picking algorithms, assess…
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 when you have received or cloned a CCS reference library (such as the DTCCSN2 library for U13C labeled lipids) bundled with lipidomics software and need to verify its…
Use when when you have paired microbiome-metabolome datasets where only a subset of metabolites carry curated biochemical annotations (e.
Use when you have imaging mass spectrometry (IMS) data preprocessed into an h5py-backed feature matrix, and a trained graph-attention autoencoder has already extracted latent…
Use when after running XCMS getEIC() to generate xcmsEIC objects and fillPeaks() to produce a filled xcmsSet object, before computing the 12 peak-quality metrics (Apex…
Use when when you have a trained molecular classifier (like BitterPredict) that accepts structured descriptor input, and you need to understand which chemical descriptor subgroups…
Use when configuring a new injection-plate design template in InjectionDesign if you have multiple QC types to position on a plate and need to visually distinguish them in the…
Use when you have a GC-MS dataset with a Match.Factor column (or equivalent quality metric) and need to evaluate how many unique compounds are retained at different confidence…
Use when after duplicate filtering and fragment length prediction (d) in ChIP-Seq analysis, when you need to convert discrete read alignments into continuous coverage signal for…
Use when you have a feature table from nontargeted LC-MS peak detection (containing m/z, retention time, and intensity values) and need to disambiguate whether detected features…
Use when you have a query MS/MS spectrum and need to identify the -matching library spectrum from a large spectral database, particularly when the research goal requires…
Use when before running HiC-Pro or similar multi-stage pipelines on a new system or environment, especially when dependency installation is not automated (e.g., not in a conda…
Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships…
Use when when you have fitted one or more regression models (linear or polynomial) to external calibration standards in MS data and need to verify model adequacy before applying…
Use when you have raw GCxGC-MS data in NetCDF format that contains instrumental and chemical noise (baseline drift, high-frequency signal artifacts) and you need to prepare…
Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical s — from…
Use when after executing an MZmine batch processing workflow on raw metabolomics
Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for…
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 have MS/MS spectra (centroided m/z and intensity pairs) and corresponding MS1 precursor masses but lack reference spectra or a priori formula information.
Use when after forking and cloning a repository (e.g., scverse/scanpy) to verify that the development environment is correctly configured, or after implementing a feature or…
Use when when you have access to a curated dataset (such as LOTUS) with published headline statistics in a peer-reviewed article or enriched index, and you need to validate data…
Use when you have experimental retention times measured on a source chromatographic
Use when you have mass spectrometry data (m/z, retention time, intensity) loaded into a Pandas DataFrame and need to explore the full 3D structure of a peak map interactively,…
Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo, Waters, or Bruker instruments) and a list of target compounds defined by precursor m/z values (and…
Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have…
Use when you have statistically significant LC-MS features grouped into structural clusters (isotopologue groups, adduct groups, cross-assay links) and correlation cluster…
Use when after peak detection on LC/HRMS data (mzXML, mzML, netCDF formats) when m/z values require refinement for improved mass accuracy in untargeted metabolomics workflows.
Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.
Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel…
Use when after running annotateRC() on LC-MS AIF features, when you need to validate whether a feature's rank-1 annotation is reliable or when you suspect that structurally…
Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix.
Use when you have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM…
Use when before peak detection on a composite or individual mass track when you need to filter out low-intensity noise and baseline drift without removing true signal.
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 after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature…
Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph…
Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D…
Use when when you have Rust source code (such as the mzPeak format implementation
Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined…
Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in…
Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass,…
Use when when you have a query electron ionization mass spectrum (as m/z and intensity pairs) and need to identify it against a spectral library stored in msp format.
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 you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
Use when you have spectrum or chromatogram data stored as XML strings (e.g., in a SQLite database indexed by spectrum ID) and need to access individual spectra by ID or iterate…
Use when when fitting a nonlinear regression (GAM spline) through retention time anchor points derived from feature pair alignments in LC-MS metabolomics, and you suspect some…