Use when when a new version or variant of a tool claims performance improvements
Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to…
Use when you have MS/MS fragmentation spectra (from Orbitrap or Q-TOF instruments) in MGF format with known precursor m/z, adduct type, and collision energy, and you need to…
Use when when you have access to the source code of a chemo-informatics tool (e.
Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a…
Use when when you have raw metabolomics measurements in tab-delimited text format (e.g., from Sciex OS exports) and need to load them into R for quality control analysis.
Use when after peak detection and feature alignment in a metabolomic LC–MS/MS or GC–MS workflow, when you have a feature table (rows=metabolic features, columns=samples) split…
Use when when you have downloaded a released version of a structured dataset (e.g., LOTUS from Zenodo) and need to confirm it matches the documented headline statistics before…
Use when after completing feature m/z grouping and pairwise alignment detection on two LC-MS datasets acquired under non-identical conditions.
Use when after loading and preprocessing a Cardinal MSImagingExperiment object (with normalized peaks and optional spatial segmentation results), and before conducting spatial…
Use when during MS/MS spectral preprocessing when converting raw spectra from .mgf, .msp, or .mzML formats into a bag-of-fragments corpus for LDA modeling.
Use when you have a filtered peak list (CSV with m/z values and assigned molecular formulas) from FT-ICR MS and want to infer biochemical transformations occurring in microbial or…
Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their…
Use when when you have deposited a collection of JSON project documents in a platform or repository and need to verify that all conform to a published JSON Schema specifi — from…
Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, and you need to identify the most likely candidate molecules from a r — from…
Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed…
Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and…
Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
Use when after downloading an mzML file from a remote repository (e.g., MetaboLights, MassIVE, GNPS) via USI resolution, before attempting to parse it into a spectrum container or…
Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
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 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 after quantifying the same read set with two versions of a mapping/quantification tool (e.g., C++ salmon 1.11.
Use when after running an end-to-end annotation workflow (matching, clustering, filtering, and prioritization) on untargeted LC-MS peak tables, when you have access to a curated…
Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce…
Use when when processing aligned LC-MS data across multiple samples where the computational bottleneck is repeated peak-detection algorithm calls (one per sample per m/z value).
Use when after uploading a sample list to InjectionDesign and before performing inter-batch balancing and intra-batch randomization.
Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular…
Use when after normalization (normalize_total, log1p transformation) and before PCA or other dimensionality reduction on raw or near-raw single-cell gene expression matrices.
Use when when you have extracted retention times from the top detected MS1 features in a LC-MS run and need to evaluate whether the gradient spreads those compounds efficiently…
Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
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 constructing or enriching a chemical formula database that must capture not just structural similarity (DBEdges) but also biological co-occurrence patterns.
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 annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches…
Use when after peak detection in GCIMS when you need to group detected peaks across multiple samples into reproducible clusters.
Use when when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or…
Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral…
Use when after creating a fresh conda environment from a pinned dependency specification (environment.yml or requirements.txt) and installing packages via conda and/or pip.
Use when you have GC–MS or LC–MS data represented as a two-dimensional map (m/z vs retention time) and need to identify analyte signals and marker features while minimizing false…
Use when when you need to enable users to express complex mass spectrometry search patterns (e.
Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when…
Use when when processing LC-MS metabolomics datasets with 10 or fewer samples and requiring reproducible mass track alignment across the cohort.
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 when a tool claims to be 'scalable' or 'performance-conscious' but lacks published performance benchmarks, or when you need to confirm that runtime and memory scale…
Use when when you need to enable non-programmers or domain experts to formulate complex, unambiguous queries over specialized data (e.
Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures…
Use when you have an experimental mass spectrum (query) and a set of molecular candidate structures, and you need to rank the candidates by how well their predicted spectral…
Use when you have peak data from MSI experiments (stored as .zip peak matrix files) where matrix ions (e.g., silver adducts in AgLDI-MSI) dominate the spectrum and obscure analyte…
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 when you need to generate a realistic LC/GC-MS feature table (peak intensity matrix) with controlled, quantifiable condition effects (e.g., differential metabolite…
Use when after completing a multi-stage Docker build targeting a compiled runtime environment (e.g., airdpro:cli produced from a Wine + .NET Framework 4.8 + Ubuntu 22.
Use when after loading raw m/z peak data (in MetaboAnalyst, MetaboShiny native, or Metabolights format) and merging it with sample metadata (batch IDs, concentration values,…
Use when when developing or extending mass spectrometry data processing workflows (e.
Use when you have a pre-trained ABCoRT model checkpoint and a new chromatography
Use when after calculating 12 peak-quality metrics on a development set of extracted ion chromatograms (EICs) and labeled peaks, when you need to select both the classification…
Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
Use when you have isolated TIC peak regions and need to extract ion chromatograms
Use when you have sampled flux distributions from two or more constraint-based metabolic models representing different biological conditions (e.
Use when you have processed MSI peak data (in rMSIproc format) and need to distinguish matrix-related ions from analyte signals.