Use when you have raw LC- or GC-HRMS data from vendor instruments (ESI or APCI ionization) that needs to be converted to a vendor-neutral format for non-target screening, or you…
Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a…
Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) in TSV or CSV format with separate 2D and 3D structure-organism pair tables, and ne — from…
Use when you have raw Bruker NMR spectral files (from a Bruker instrument) in a directory and need to prepare them for automated metabolite identification and quantification using…
Use when when you have preprocessed MS/MS spectral peak data (m/z and intensity pairs) and need to compute a complexity metric for individual spectra prior to similarity…
Use when when applying iterative peak detection (local-maximum or Gaussian-fit methods) to 1D extracted ion chromatograms (XICs), arrival time distributions (ATDs), or MS1 spectra…
Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type…
Use when you have a chromVARDeviations object with multiple annotation sets (such as JASPAR motifs and kmers) and need to determine which annotation pairs are redundant (high…
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 need to systematically enumerate all possible lipid species within a defined analytical scope—specifically when you have specified one or more lipid classes (e.g.,…
Use when you have LC-MS/MS data in mgf format and a custom spectral database prepared with CFM-id (or an in-built database), and you need to identify unknown compounds by…
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 when you need to confirm that a publicly hosted academic web service (such as molDiscovery) is live and responding at a documented endpoint URL, or when troubleshooting…
Use when you have imported a raw LA-ICP-MS raster image (line-by-line, spot-wise, or ablation-time-aligned format) and need to isolate tissue regions from instrumental background…
Use when you have raw MRM sample files from a LC-MS/MS instrument and need to systematically recover all precursor m/z and product m/z pairs for each transition.
Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
Use when when you have mass spectrometry data stored in non-standard formats (SQLite, HDF5, custom binary) that pymzML does not natively support, and you want to enable…
Use when you have selected statistically significant features from multi-assay untargeted LC-MS metabolomics data and need to group them by structural relationships defined by…
Use when when you have quantitative lipidomics data (either from Skyline CSV export or numerical matrix format) with sample annotations and a biological grouping variable (e.
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 downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS,
Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z…
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 after running GNPS molecular networking, SIRIUS compound identification,
Use when you have constructed or received a SummarizedExperiment object (or similar S4 class) containing MS feature tables, counts matrices, or sample-level metadata, and need to…
Use when you have computed raw or standardised correlation scores (or other link-ranking metrics) for all possible GCF-MF pairs in a dataset and want to verify that validated…
Use when you have multiple LC-MS runs with the same set of targets (compounds) and observe or expect retention time drift or jitter between runs.
Use when you have MS/MS spectra with high chemical noise (spurious ions arising from incomplete ionization, in-source fragmentation, or instrument artifacts) and you possess…
Use when when you have raw untargeted LC-MS metabolomics data and need to detect low-quality or mis-integrated peaks in an XCMS-processed xcmsSet object before performing…
Use when you have raw mass spectra or processed feature matrices from liquid chromatography–mass spectrometry (LC-MS) or direct infusion MS that must be ingested by a deep…
Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.
Use when when you have computed z-score deviations for genomic annotations (e.g., motifs) across multiple cells or samples and need to quantify uncertainty in their variability…
Use when you have a parsed sample list with metadata (sample IDs, classification
Use when you have a collection of records in a standardized format (e.g., MassBank plain-text or structured records) that must be validated before commit or publication.
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 a large mass spectrometry dataset stored across multiple mzML, mzXML, or CDF files and need to perform operations (e.g., normalization, filtering, feature…
Use when when you have multi-omic TWIM-MS data (raw or processed arrival-time records) and have already assigned features or detected ion features to biomolecular classes (e.
Use when you have implemented a new RDKit-based ComputeConverter for SMILES↔InChI conversions and need to verify that the conversion methods preserve molecular structure integrity…
Use when you have pairs or triplets of MS/MS spectra with associated metadata (compound structural information, Tanimoto similarity scores) and want to learn embeddings that…
Use when when a new version or variant of a tool claims performance improvements
Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1,…
Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential…
Use when you need to verify that a Python package (or similar installable software) passes its declared integration test suite as a prerequisite to trusting its reliability in…
Use when when you need to reconstruct or validate the control-flow architecture of a spectral search system that must handle both exact-match library lookups and analogue…
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 you have a raw metabolomics abundance table (e.g., LC/MS or GC/MS peak intensities or concentrations) with non-normal distributions and missing values, and you need to…
Use when when you have a peptide sequence and need to predict which fragment ions (B and Y series) should appear in an MS2 spectrum at a known isotopic abundance (e.g., natural…
Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected)
Use when you have raw or annotated MS/MS spectra (in MGF, mzML, or mzXML format) destined for de novo peptide sequencing with Casanovo.
Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in…
Use when when you have coordinate-sorted BAM files from single-cell ATAC-seq experiments (e.g., 10X Genomics scATAC-seq) and need to generate a compressed fragment file for…
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 before constructing a DESeqDataSet from any count matrix (whether from tximport, HTSeq, featureCounts, or raw counts).
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the n — from…
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 after structural clustering (isotopologue grouping, adduct detection, cross-assay linking) and correlation clustering of LC-MS features, when you need to inspect and…
Use when you have deployed a TensorFlow model via TensorFlow Serving in a containerized environment (e.
Use when when working with JSON project documents that must conform to a schema-defined structure, and you need to apply type-specific validation, sanitization, or transformation…
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…