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 you have a normalized abundance matrix from LC-MS/MS profiling with sample class assignments (e.g., phenotypic groups, disease states, treatment conditions) and need to…
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 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 mass spectrometry run data (spectra, chromatograms, instrument metadata) that must be stored in or recovered from the mzPeak format, or when you need to validate…
Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
Use when you have Nightingale Health 1H-NMR metabolomics assay output (metabolite concentrations in a samples × features matrix) and you want to compute a published metabolic risk…
Use when you have raw MS data in vendor formats (Agilent .d, Thermo .raw, Bruker .
Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those…
Use when you have two separate LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to establish feature-to-feature correspondence…
Use when after converting a decision tree path into a MassQL query string, before deployment to production mass spectrometry workflows.
Use when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each…
Use when when you have tandem mass spectra (MSMS) from related or candidate molecules and need to determine which similarity metric—cosine, modified cosine, or neutral loss— ranks…
Use when when you have run ORA on a metabolomics dataset and obtained p-values for pathway enrichment, but you need to assess whether observed significance is genuine or an…
Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate…
Use when when you need to inventory a collection of related web applications or tools distributed across multiple repositories, discover their live deployment URLs, trace their…
Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to…
Use when when a statistical method offers a parameter to trade computational cost for precision (e.
Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.
Use when when evaluating a regression or similarity prediction model and you need to understand whether prediction error is uniform across the outcome space or concentrated in…
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 you have raw GC-MS data with overlapped peaks in a specific retention time region and need to resolve the individual pure mass spectra of all components present in that…
Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5…
Use when you have a collection of molecular structures (as SMILES or SDF files) and need to generate pre-computed CCS values for fast retrieval in downstream mass spectrometry…
Use when after fitting candidate GAM splines with B-spline basis functions across a range of basis dimensions (k values 12–20) to anchor feature pairs (m/z and retention time…
Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100…
Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability…
Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format and need to identify similar spectra for clustering, but exhaustive pairwise cosine-similarity…
Use when you have NMR metabolite measurements from peripheral blood samples (plasma/serum) paired with processing delay metadata (pre-centrifugation and post-centrifugation times)…
Use when you have a characterized lipid species (with defined class and fatty acid composition) and need to predict which adduct forms will ionize under your experimental…
Use when when you have obtained a raw Orbitrap mass spectrometry file and need to verify that the instrument was configured as claimed in the methods section or dataset…
Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings.
Use when you have raw GC–MS or LC–MS data in two-dimensional m/z vs retention time format and need to identify marker features at parts-per-billion sensitivity without relying on…
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 you have deployed a TensorFlow model via TensorFlow Serving in a containerized environment (e.
Use when you have RNA-seq read counts (FPKM or similar) for multiple cell lines or biological samples, a genome-scale metabolic model with GPR associations, and you need to…
Use when you have a metabolomics count table (rows=metabolites, columns=samples)
Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d) or UIMF format with jagged peaks and low-abundance ions that require signal enhancement, but you need to…
Use when when you have molecular input data available in two or more distinct formats (e.g., RDKit-extracted fingerprints AND torch_geometric Graph objects representing molecular…
Use when when you have retrieved a large, heterogeneous collection of tandem MS files from ReDU or MassIVE and need to isolate a subset sharing specific sample characteristics (e.
Use when you have Nightingale Health 1H-NMR metabolomics measurements for a new cohort and wish to compute one or more established metabolic risk scores (mortality, MetaboAge,…
Use when you have preprocessed (smoothed and baseline-corrected) 2D-GCxGC-MS chromatograms from multiple samples and need to align their peak positions to a common reference…
Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score…
Use when when you have loaded a structure-organism pairs table from a natural products database (e.g., LOTUS) and need to answer questions about the distribution of chemical…
Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d)
Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
Use when when you have extracted peak tables from multiple independent LC/HRMS analysis batches (each with retention time and m/z values) and need to align peaks across batches to…
Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.
Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex…
Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across…
Use when processing extracted peak lists from MSI data and you need to annotate matrix-related signals but suspect that multiple ions with the same or very similar m/z values…
Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify…
Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to…
Use when you have a spatial transcriptomics dataset (AnnData object) with cell/spot coordinates and an associated tissue microscopy image file, and you need to compute…
Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon…
Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using…
Use when you have completed cross-validation tuning of one or more machine-learning
Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign…
Use when when you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format…