Use when when you need to empirically validate that one mass spectrometry data processing library achieves higher throughput than competing alternatives.
Use when you have identified one or more proton NMR spectral regions-of-interest
Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to…
Use when when comparing two implementations of the same RNA-seq mapping algorithm on identical reference indices and read sets, if per-read mapping agreement is <99.8% or the…
Use when designing or validating a metabolomics pathway analysis experiment, especially when you have uncertainty about how many metabolites your detection platform will reliably…
Use when you have a set of query chemicals and a reference library (organized by type or group), and you need to determine which reference compounds most closely resemble each…
Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names…
Use when after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or…
Use when you have loaded a raw or partially processed MsmsSpectrum object and need to reduce spectral noise before annotation, matching, or visualization.
Use when you are setting up a new LipoCLEAN analysis for MS-DIAL output and need to create a configuration file tailored to your MS-DIAL version (4 or 5).
Use when when you have domain-specific functionality (e.g., spectral similarity scoring, peak detection algorithms) implemented in one language (Python) but need to make it…
Use when evaluating whether a published computational method can be independently executed: (1) source code is claimed to be available but repository structure, build…
Use when you have generated 1D FID time-domain data and Fourier-transformed frequency-domain 1H NMR spectra, or computed 2D COSY/HSQC correlation matrices, and need to write them…
Use when you have a tabular file (CSV or Excel) that has been manually or semi-automatically tagged with export tags, and you need to verify tag correctness before running the…
Use when when you have preprocessed MS/MS spectral data (filtered, noise-reduced,
Use when when you have separate LC-MS peak tables for unlabeled (C12) and labeled (C13) isotope tracer experiments and need to identify which features correspond to the same…
Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
Use when immediately after importing raw LC-MS peak tables (e.g., Progenesis format) and before applying group or replicability filters.
Use when when you need to create in silico LC-MS/MS experiments with diverse chemical backgrounds for testing fragmentation strategies or acquisition controllers, and you want the…
Use when when you have peripheral blood sample cohorts (plasma/serum) with multiple timestamps (e.
Use when when training a deep neural network on mass spectrometry spectral data where overfitting is a risk (especially with data augmentation applied), and when you need both…
Use when you have raw MS/MS spectra in MGF or other standard formats that need to be ingested into a machine learning pipeline for cross-modal matching against molecular…
Use when when preparing multi-formula MS/MS training data for a rescore model, if the raw positive examples show extreme imbalance (some formulas represented by hundreds of…
Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into…
Use when you have a chemical substrate and need to predict its biotransformation
Use when annotating metabolites in untargeted metabolomics experiments where both established biochemical pathways and experimental MS2 similarity patterns must be simultaneously…
Use when when you have extracted ion chromatograms (XICs), ion mobilograms (IMs), or mass spectra from diaPASEF or other DIA workflows and need to visualize them interactively to…
Use when when you have synthesized or assembled mass spectrometry spectral data (m/z values, intensities, retention times) and need to encode it as a portable, standard mzML file…
Use when you have retention time predictions from a source chromatographic method and need to predict retention times for a target chromatographic method, but have limited…
Use when when preparing raw MS/MS spectra for input to a Siamese neural network trained to predict structural similarity scores (Tanimoto).
Use when after generating aligned MS2 fingerprints (sample-by-fingerprint matrices) from metabolomics data when you need to visually inspect sample clustering, identify sample…
Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
Use when you have parsed LC-MS/MS spectral data (precursor m/z, ionization mode, collision energy, and a list of fragment m/z and intensity pairs) and need to submit it to the…
Use when augmenting mass spectrometry ion images for contrastive learning, particularly when the model must generalize across different detector conditions or signal-to-noise…
Use when you have a GC-MS dataset with Match.Factor scores for each detected compound (output from Agilent Unknowns Analysis or equivalent), and you want to reduce the number of…
Use when after training a customized R statistical or machine learning model on annotated training data, you need to persist the trained model object for reuse in downstream…
Use when you have Thermo Fisher Scientific .raw files from an LC-MS experiment and need to extract spectral features (base-peak m/z, intensity, scan-level properties) indexed by…
Use when when you need to prepare mass spectra and molecular structures for joint modeling in a BART or transformer-based sequence model, and you lack a unified representation…
Use when after integrating transcriptomics-derived (RAS), metabolomics-derived (RPS), and extracellular flux constraints into cell-relative metabolic models, sample the feasible…
Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate…
Use when immediately after acquiring raw GCxGC-MS data in NetCDF format (.cdf files) and before any signal enhancement (smoothing, baseline correction) or alignment steps.
Use when you have a pretrained RT-Transformer model checkpoint from a large, well-characterized chromatographic dataset (e.g., SMRT) and need to predict retention times for a…
Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.
Use when immediately after automatic peak detection on a raw or processed MS spectrum when you have a list of candidate peaks with m/z and intensity values but lack systematic…
Use when after peak detection when you have a detected peaks table with m/z values and need to correct systematic mass drift or inaccuracy before peak alignment across multiple…
Use when you have generated a peak table or feature list output file from an external peak-picking tool (MZmine, XCMS, MS-DIAL, or Compound Discoverer) in its native export format…
Use when you have a pre-trained GNN model for CCS prediction and need to verify that it generalizes to test data that was held out during training.
Use when you have a tab-delimited feature table (m/z, retention time, intensities) from LC-MS preprocessing and need to group related ions (isotopologues, adducts, in-source…
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 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 raw LC-MS/MS data in mzML or mzXML format and need to isolate specific MS1/MS2 scan pairs for a targeted compound list or for building a local spectral library.
Use when you have tab-delimited metabolomics data with columns for aliquot identifiers, compound names, peak areas (primary and internal standard), sample type (QC, study sample,…
Use when you have a raw or preprocessed single-cell count matrix (from BAM-to-fragment or FASTQ-to-matrix pipelines) and need to apply matrix-free algorithms like tl.spectral,…
Use when after library-matching has produced ranked candidate spectra with MS2Deepscore embeddings.
Use when you have MS2 product-ion spectra in open formats (.mzML or .mzXML) from public mass spectrometry datasets (e.g., from MassIVE with a valid accession) and need to identify…
Use when you have a MemoMatrix (sample-by-fingerprint matrix) from aligned MS2 spectra and need to visually compare sample similarity or clustering patterns, especially when…
Use when you have raw GCxGC-MS chromatogram data in NetCDF format from multiple samples (e.g., case and control groups) and need to prepare them for multivariate analysis such as…
Use when your metabolomics experiment includes calibration line samples with known concentrations for spiked compounds, and you have computed batch-corrected…
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 raw metabolomics peak intensity data exhibits right-skewed distributions