Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from…
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 processing spectral datasets from open mass spectra libraries (OMSLs) where structural identifiers and ionization metadata are incomplete or inconsistent.
Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with…
Use when you have two spatial omics datasets (e.g., spatial transcriptome and metabolome spot matrices) collected from the same or adjacent tissue sections, with both feature…
Use when you have loaded mzML.gz or HDF5-formatted raw LC-IMS-MS/MS data and need to identify discrete peaks before feature alignment.
Use when you have generated a GNPS molecular network (classical or feature-based
Use when when you have untargeted GC–MS or LC–MS data in the form of a two-dimensional m/z vs retention time map and need to identify marker features without conventional peak…
Use when you have MS data in a new format or storage system (e.g., a custom database, HDF5 file, or proprietary raw file) and need to make it accessible to Spectra-based analysis…
Use when you have isolated reference peaks from training chromatograms (ground-truth, single compounds per sample) and need to create a diverse, labelled training set large enough…
Use when after discovering Mass2Motifs through LDA topic modeling of MS/MS fragmentation data, when you need to assign chemical meaning (substructure classes, candidate…
Use when after running tardisPeaks() with screening_mode=TRUE on centroided .mzML LC-MS data, when you need to visually inspect whether the 10 target compounds (internal standards…
Use when your metabolomics dataset (LC/MS or GC/MS) contains missing values encoded as NA or zero that represent compounds below the instrument's limit of detection (LOD) or limit…
Use when you have normalized gene expression data (log-transformed, quantile-normalized) from a time-course or case-control experiment, a ranked gene statistic (e.g., mean…
Use when you have paired in silico and experimental measurements from multiple biological samples (e.
Use when after preprocessing and aligning 2D chromatogram data (baseline correction, smoothing, peak alignment) and after running m_prcomp multiway PCA on the joined chromatogram…
Use when you have a cooler Hi-C contact matrix, a set of genomic features (e.g., CTCF peaks, enhancers, or TAD boundaries defined in BED format), and want to quantify average…
Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs.
Use when after anchor selection and RT mapping spline fitting, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to determine which…
Use when after loading MS-Dial feature tables (e.g., Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt) and before sample-level filtering or imputation, whenever the feature…
Use when after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
Use when when importing a tab-delimited or Sciex OS text export metabolomics dataset into mzQuality, before building the SummarizedExperiment object.
Use when after running ModiFinder's probability generation on a known compound–modified compound pair, you have a vector of per-atom modification probabilities and need to…
Use when after running retention-order prediction experiments on a test or held-out evaluation dataset.
Use when after peak detection and clustering have been completed on aligned and baseline-corrected GC-IMS data, and before imputation or statistical analysis.
Use when when processing MS1 mass tracks from a single sample and you have already constructed per-bin mass tracks with consensus m/z and intensity vectors.
Use when you have configured a GitHub Actions workflow that executes build, test, and quality checks, and you want to embed a machine-readable, auto-updating badge in your…
Use when after MS2 fingerprints have been generated by counting MS2 peaks and neutral losses in each sample, and you have aligned them into a MemoMatrix (sample-by-fingerprint…
Use when you need to add a new local chemical structure conversion capability to MSMetaEnhancer when existing web-service converters (CTS, CIR, PubChem) are unavailable, too slow,…
Use when after peak detection in untargeted LC/HRMS workflows, when you have a list of candidate peaks with signal intensity profiles and need to filter them according to data…
Use when when beginning preprocessing of a new LC-MS dataset with mzML files or raw acquisitions and you need to determine which ionization mode was used before running feature…
Use when you have extended a metabolite identification tool (such as Met-ID) to support a new derivatizing matrix beyond the default (e.
Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de…
Use when you need to set up a cloned or downloaded scientific Python package for local development, testing, or execution.
Use when apply PCA when you have a log-normalized, scaled gene expression matrix from highly variable genes and need to reduce dimensionality before constructing k-nearest…
Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other…
Use when you have raw microbiome (e.g., 16S rRNA or metagenomic) or metabolomic count tables (samples × features) and plan to train predictive models (e.g., MiMeNet, linear…
Use when you have a set of chemical compounds (with known retention times and intensities) loaded into a ViMMS IndependentMassSpectrometer and need to simulate a specific MS/MS…
Use when you have processed MSI peak data (in rMSIproc format) and need to distinguish matrix-related ions from analyte signals.
Use when your research proposes a new spectral embedding, matching algorithm, or retrieval method and you need to quantify its improvement over known baselines.
Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for…
Use when you have an untargeted metabolomics dataset with a two-layer network topology already constructed (one layer representing biochemical knowledge/pathways, the other…
Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
Use when you have acquired tunemix data (positive or negative ion mode, in .h5 format) with known CCS reference values and need to construct a calibration function that will later…
Use when you have adapter-trimmed FASTQ files and need to obtain transcript-level
Use when after implementing or modifying a numerical compression codec (such as MSNumpressCoder for m/z and intensity arrays in mass-spectrometry workflows) to verify that…
Use when after constructing a peak properties dictionary via csv_to_peak_properties
Use when after obtaining shrunken or unshrunken log fold change estimates from DESeq2 results objects, particularly when comparing multiple shrinkage estimator types (apeglm,…
Use when when a metabolite feature has been assigned a top-rank lipid annotation (e.g., LPC(14:0)) but you need to assess whether related lipid species containing the same fatty…
Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions…
Use when you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect…
Use when when you have trained a predictive model (e.g., neural network or regression model) that outputs continuous scores (such as Spearman correlation coefficients) for…
Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion…
Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural…
Use when when you have ranked gene statistics and gene set collections, and your analysis requires P-value discrimination below a fixed lower bound (e.g., distinguishing between…
Use when preparing ion image data for contrastive learning in mass spectrometry imaging (MSI), specifically when you need to augment single ion images into pairs of variants for…
Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the…
Use when you have received a USI string (formatted as mzspec:<namespace>:<resource>:<identifier_type>:<identifier>)
Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from…
Use when apply SSC when you have preprocessed and normalized MS imaging data (e.g., after TIC normalization and peak processing) and need to discover spatially distinct metabolite…