Use when you have at least 3 raw mass spectrometry samples in open formats (mzML, mzXML, CDF) from untargeted metabolomics experiments and need to configure parameters for XCMS,…
Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and…
Use when you have an annotated list of metabolite compounds (with associated m/z features or compound IDs) and want to determine which KEGG metabolic pathways are significantly…
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 when constructing a reference mass-matching framework for untargeted metabolomics or isotope-tracing LC-MS data, before pattern-matching observed features to isotopic and…
Use when after m/z grouping and pairwise alignment detection when you have a metabCombiner object containing candidate feature pair alignments and need to select a subset of…
Use when you have a 1D ¹H NMR spectrum (as chemical shift vs. intensity) and a corresponding peak list (chemical shift values), and you need to identify which metabolites are…
Use when you have paired experimental and computational predictions for the same biological property (e.
Use when when you need to understand or modify how MS2Query routes query spectra through its dual-pathway architecture, or when integrating MS2Query into another tool and need to…
Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or…
Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks…
Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for…
Use when you have a GNPS-generated molecular network (classical or feature-based
Use when you have a published research article describing a new FT-ICR MS analysis tool and need to verify which analytical and visualization features are actually implemented…
Use when when you have loaded both a known compound and its modified analog with MS/MS spectra, initially generated baseline modification probability scores, and then obtained or…
Use when when you have a Spectra object backed by an on-disk MS data source (e.g., MsBackendMzR reading mzML, mzXML, or CDF files) and need to process large numbers of spectra in…
Use when when you have both an observed NMR mixture spectrum and a candidate reconstructed spectrum (each represented as intensity distributions across chemical shift bins), and…
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 exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
Use when when you need to construct a dual-branch neural network encoder that processes two augmented versions of the same input (e.g., ion images in COL or ISO mode) and must…
Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified…
Use when you have xcms-processed LC-MS data with detected feature groups (from xcms grouping), suspect retention time misalignment across samples due to long acquisition periods…
Use when raw metabolomics peak intensity data exhibits right-skewed distributions
Use when when you have processed LC-MS data through XCMS alignment but suspect misaligned features due to retention-time drift over long acquisition periods (>1 week) or large…
Use when when you have a chromVARDeviations object with multiple annotation sets (e.
Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity,…
Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library…
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 raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication,…
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…
Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or…
Use when when you have a pre-trained model and need to report stable, generalizable performance on a fixed training set with multiple held-out test splits.
Use when when you have a USI (e.g., mzspec:MTBLS1124:QC07.mzML) pointing to a public mzML or related spectrum file in MetaboLights, MassIVE, or GNPS repositories, and need to load…
Use when after generating cross-spectrum negative examples via precursor m/z windowing and before training a rescore model (e.g., Siamese architecture in FIDDLE v2.0.0).
Use when after peak detection and feature table generation when you have a collection of m/z, retention time, and intensity values and need to identify which features are related…
Use when you have a two-dimensional MS map (m/z vs retention time) from GC–MS or LC–MS data and need to discriminate analytes and identify marker features without false positives…
Use when you have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality of the peak matrix…
Use when after feature m/z grouping and pairwise alignment detection have identified candidate feature pairs, and anchor points have been selected to establish retention time…
Use when after installing a Python package (especially one with optional dependencies) to confirm that: (1) core modules are accessible and importable;
Use when you have a normalized gene expression matrix (genes × samples) and an experimental design with known treatment groups or conditions, and you need to estimate the effect…
Use when you need to evaluate whether a newly released or candidate library (e.g., spectrum_utils v0.4.
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 have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and…
Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum…
Use when you have collected or inherited sample-information metadata from multiple sources (e.
Use when you have a collection of molecular fingerprint vectors (such as biosynfoni count fingerprints) and need to measure structural similarity between all pairs of molecules.
Use when when you have extracted intermediate JSON conforming to the Experiment Description Specification and need to restructure, filter, sort, or aggregate records (e.
Use when you have paired microbiome-metabolome (or similar multivariate) datasets and want to quantify whether training on a superset of features (e.g., both annotated and…
Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a…
Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar…
Use when you have raw electron ionization mass spectra (m/z and intensity pairs) that you intend to match against a library using the Identity (EI Normal) or Similarity (EI…
Use when when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages,…
Use when you have statistically significant LC-MS features (e.g., filtered by p-value < 0.01) from multi-assay metabolomics datasets and need to group features that represent the…
Use when when processing LC-MS data from isotope labeling experiments where the tracer (13C, 2H, 15N, 18O, or 34S) has known isotopic impurity and you observe discrepancies…
Use when you have a ranked list of metabolite identifiers (PubChemCIDs, KEGG IDs, or chemical names) from differential abundance or ANOVA testing and need to determine which…
Use when you have a SMILES string or batch of SMILES strings representing chemical structures and need to obtain NP Classifier predictions programmatically.
Use when you have generated a GNPS molecular network (classical or feature-based
Use when a scientific Python package is being moved to a new GitHub organization with different structural conventions (e.g., from a personal lab account to a community-led…
Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measure — from…
Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a…