Use when analyzing GC-MS data containing overlapping chromatographic peaks—a common scenario in untargeted metabolomics and environmental screening where sample complexity or…
Use when you are preparing to reuse public tandem MS data from MassIVE via ReDU and need to partition files by sample metadata (e.g., organism, tissue type, extraction method,…
Use when you have 1H NMR spectral tensors as input and need to extract local features (e.g., peak patterns, signal neighborhoods) before applying attention-based or sequence-level…
Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover con — from…
Use when you have a metabolomic SummarizedExperiment object with replicate QC (quality control) samples and need to remove non-reproducible metabolic features before phenotype…
Use when when you need to validate that a Python package (or update to it) is accessible to end users through official distribution channels, or when you are preparing a release…
Use when you have a pretrained deep learning model, a reserved test set with ground-truth annotations, and need to evaluate prediction quality or generate embeddings for…
Use when you have access to a published study that provides a Jupyter notebook (.ipynb) containing executable code for reproducing simulations, analyses, or figures, and you need…
Use when using Casanovo for de novo peptide sequencing on high-stakes datasets (immunopeptidomics, paleoproteomics, or monoclonal antibody discovery) where missing the correct…
Use when when you have raw mass spectrometry imaging data tensors and need to build a trainable deep-learning classifier that outputs class probabilities (tumor vs.
Use when when preparing XCMS peak tables for quality classification and you observe that the default RSD threshold (0.3 or 30%) is either too permissive (retaining noisy EICs) or…
Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR…
Use when when you have loaded an LC-MS spectrum file (mzML, mzXML, or equivalent) into the GNPS LCMS Visualization Dashboard and need to annotate extracted ion chromatograms with…
Use when you have acquired a versioned QC workflow definition file (YAML or JSON) from a metabolomics QC system release (e.g., v1.0.
Use when you have untargeted metabolomics mass spectrometry data (MS2 spectra with m/z values and intensities) and an existing knowledge-driven metabolite network, and you need to…
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
Use when you have a matrix of Nightingale Health 1H-NMR metabolomics measurements (samples × features) and need to generate predicted metabolic scores published in peer-reviewed…
Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage,…
Use when after training a NeatMS neural network model on labelled peak data (High_quality, Low_quality, Noise) and you need to determine the optimal probability threshold for…
Use when you have raw tabular experimental data (CSV or Excel) with column headers annotated using MESSES tag syntax (#<table_name>.id for record identifiers, #.
Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query''s two-branch workflow split) modified the codebase architecture, control flow, or data…
Use when you have fitted a linear model to gene expression data (microarray, RNA-seq, qPCR, or proteomics) across multiple samples and need to compute gene-level test statistics.
Use when when you have multiple batches of metabolomics data in SummarizedExperiment
Use when you have a trained neural network model and a labelled validation dataset (with high-quality and low-quality peak annotations), and you need to determine the optimal…
Use when you have detected monoisotopic features (m/z, drift_time, retention_time,
Use when you have CE-MS raw data in OnDiskMSnExp format with both positive and negative polarity acquisitions, migration times that vary due to electroosmotic flow drift, and…
Use when when you have completed an initial ModiFinder analysis on a compound pair (known compound + modified analog with unknown structure), and you subsequently acquire or…
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 you have peak intensity vectors from LC/GC-MS experiments with corresponding QC (quality control) sample measurements, and you need to correct for batch…
Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which…
Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format)…
Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or…
Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile)
Use when after constructing a peak properties dictionary via csv_to_peak_properties
Use when after completing PCA and k-nearest neighbor graph construction on preprocessed, log-normalized, highly-variable-gene-filtered single-cell RNA-seq data (stored in an…
Use when after nontargeted peak detection and segmentation has generated a feature table from raw LC-MS data (mzML or vendor format), apply quality assessment when you need to…
Use when when you have raw Agilent MassHunter (.d) or UIMF IM-MS data files from drift tube (DT) or structure for lossless ion manipulations (SLIM) instruments and need to ingest…
Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment…
Use when when you have LC-MS/MS data in Mascot Generic Format (mgf) files and need to identify compounds against a curated custom database (e.g., prepared using CFM-id for a…
Use when when you have a feature table from LC-MS preprocessed data (e.g. from asari v1.9.2) and need to annotate ions and infer neutral mass.
Use when you have MS2 spectra data (MGF/mzML format) and aligned feature tables, and your analysis goal is to compare samples that may have poor MS1 feature overlap, strong…
Use when evaluating the reliability of non-targeted data pre-processing (NPP) tools (XCMS, MZmine 2, MS-DIAL, etc.) on known metabolite peaks.
Use when when you have access to source code or algorithmic documentation of a metabolite generation pipeline (such as MAGMa's job subproject) and need to understand, validate, or…
Use when when you have a query electron ionization mass spectrum (m/z and intensity pairs) and need to identify the most similar spectra from an MSP-formatted spectral library.
Use when when you have a processed or annotated MsmsSpectrum object (from USI loading or direct instantiation) and need to generate a figure showing observed peaks, their…
Use when when you have a list of chemically known compounds and need to validate that an MS processing pipeline (e.g., mzExacto) correctly retrieves their characteristic m/z,…
Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
Use when when you have filtered ATAC-seq or DNAse-seq peak counts (after GC bias correction, sample filtering, and peak filtering) and wish to measure how strongly each annotation…
Use when after peak detection on composite mass tracks when you need to evaluate whether a detected peak represents a pure, interference-free signal on its m/z channel.
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 before running HiC-Pro's normalization stage on aligned Hi-C BAM files. Specifically, when you have SAM/BAM-formatted aligned Hi-C reads that need bias correction and…
Use when when you have ionized adduct structures (SMILES or MOL format) from an ionization-state determination step and need to create an ensemble of relaxed 3D geometries for…
Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess…
Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for…
Use when you have two co-registered LA-ICP-MS element channel images and need to quantify whether their spatial distributions are statistically correlated or independent.
Use when when you have raw ion mobility-mass spectrometry data (drift times, m/z values, and frame metadata) from DTIMS-MS, TWIMS-MS, or SLIM-based instruments and need to compute…
Use when when you have downloaded raw spectroscopic datasets from multiple sources (NMR, HSQC, COSY, IR files) and need to combine them into a single coherent training corpus…
Use when after extracting and optionally combining MS2 spectra from a chromatographic peak (e.g., at a known m/z value like 304.1131), you need to determine which compound(s) in a…
Use when when XCMS or other DTW-based aligners have produced misaligned LC-MS feature groups across hundreds of samples or long acquisition periods (>1 week), particularly when…
Use when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) in memory or on disk, a trained CNN model checkpoint available, and you ne — from…