Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
Use when when you have microarray or RNA-seq expression data paired with phenotype/sample metadata describing experimental conditions, treatments, or group assignments, and you…
Use when you have a large compressed scientific data file (e.g., indexed gzip mzML) where you need to retrieve specific spectra, chapters, or records by integer ID without loading…
Use when after converting or filtering objects (e.g., transformation products to suspect lists, feature groups through componentization) and before passing them to downstream…
Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative…
Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification,
Use when when you have implemented a binary file format encoder (such as igzip header construction) and need to verify that the binary output is correct before deploying it to…
Use when you have raw MS2 spectra from a sample and need to collapse them into a single sample-level representation for comparison across multiple samples, particularly when…
Use when designing a metabolite annotation workflow that must simultaneously leverage established biochemical knowledge (pathway databases, reaction networks) and experimental…
Use when when clustering large-scale mass spectrometry datasets (millions of MS/MS spectra in MGF format) where runtime is a bottleneck and you have access to NVIDIA GPU resources…
Use when you have a repository of structured records (e.g., mass spectrometry data, metadata, or domain-specific formats) and need to enforce validation rules systematically…
Use when when preparing NMR datasets for processing in NMRFx and the Dataset.createDataFile() method must choose among competing storage backends.
Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field…
Use when when configuring a multi-well plate design (96-well, 384-well, or other format) in InjectionDesign for LC/GC-MS analysis and you need to specify whether analytical…
Use when you have tandem MS data with technical replicates and need to remove features showing high variability between replicates.
Use when you need to compile and test a .NET-based metabolomics or bioinformatics
Use when when you have a metabolite SMILES structure and need to predict which adduct ions will appear in a mass spectrum acquired with a chemical derivatizing matrix.
Use when a Python package has been relocated to a new repository location, reorganized to conform to new organizational standards (e.g., metabolomics-cloud conventions), or its…
Use when when you have mzML spectrum XML already parsed (either from a file, a database query, or an in-memory representation) and need to construct Spectrum or Chromatogram…
Use when after completing feature annotation and reaction assignment in an untargeted metabolomics workflow, specifically when you have a feature-by-sample intensity matrix…
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 acquired raw SIMS (secondary ion mass spectrometry) metabolite images aligned with tissue regions and segmented single-cell masks, and you need to extract…
Use when you have LC-MS normalized intracellular metabolite abundance data from multiple cell lines (or samples) and need to compute reaction-level propensity scores that account…
Use when you have extracted MS/MS spectra for a given metabolomic feature across multiple replicates (e.g., after top-TIC filtering) and need to identify which fragments are…
Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata…
Use when after GNPS spectral library matching has been completed on a batch of MS2 spectra from public MassIVE datasets and you need to aggregate chemical annotations into a…
Use when you have time-resolved DBDI-MS data (intensity matrix with m/z features as rows and scan timepoints as columns) from direct injection analysis where chromatographic…
Use when you have completed parallel QUICK quantum calculations on multiple conformers filtered by ASE-ANI and need to extract electronic properties from the output logs and…
Use when when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated…
Use when when a software tool is distributed as a Docker image and you need to confirm it is available on a registry (e.g., Docker Hub), that the image pulls without corruption,…
Use when when you have a target compound (modified or unmodified) and need to obtain its experimental MS/MS spectrum and metadata to serve as a known reference for ModiFinder…
Use when converting MS/MS spectra into Spec2Vec embeddings using a pre-trained Word2Vec model that was trained on reference data (e.g., a subset of GNPS or MassBank).
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 comparing mapping outputs between two selective-alignment implementations (e.g., C++ vs.
Use when when training embeddings from MS/MS spectra data where you need both discriminative power (to distinguish similar spectra) and reconstruction accuracy (to preserve peak…
Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
Use when when preparing ion images (single-channel 2D arrays or multi-channel spectral images) from mass spectrometry imaging for contrastive learning in DeepION's COL or ISO…
Use when after training or evaluating a classification model (e.g., MS2DeepScore
Use when you have raw metabolomics mass spectrometry data in mzML or mzXML format and need to extract, align, and normalize metabolic features across multiple samples or…
Use when after drift correction and before imputation, when you have a MetaboSet object with LC-MS peak abundances and need to remove features with insufficient detection…
Use when you have GC–MS or LC–MS data represented as a two-dimensional map (m/z vs retention time) and need to identify analyte signals and marker features while minimizing false…
Use when when processing raw chromatography–mass spectrometry data (GC–MS or LC–MS) as a 2D m/z vs retention time map and you need to identify and visualize marker features for…
Use when after preprocessing, imputation, and batch correction of LC-MS peak tables when you need to group redundant or related feature measurements (e.g., [M+H]+ and [M+Na]+…
Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted…
Use when after running qc_summary() on a filtered mpactr object when you need to understand the distribution of ions across filter status categories (passed vs.
Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you need to link individual m/z features into structural clusters represent — from…
Use when after AutoTuner has completed EICparams extraction and parameter estimation on raw untargeted metabolomics data (mzML, mzXML, or CDF format), and you need to pass those…
Use when when you need to confirm that a research tool or package maintains a functioning test suite, especially before adopting it for downstream analysis or before contributing…
Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and…
Use when after RAMClustR clustering of XCMS-detected features and prior to final compound annotation, when you need to verify the robustness of molecular weight inference or when…
Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated…
Use when you have loaded a feature-by-pixel intensity matrix from an MSI HDF5 container and need to perform dimension-preserving corrections (e.
Use when you have processed and quantified MSI data from one or more imzML files in LipidQMap and need to export them as a unified, standards-compliant HDF5 container that…
Use when after running a ViMMS Environment simulation with save_eval flag enabled, when you need to preserve the link between each simulated MS/MS scan in the output mzML file and…
Use when after running annotateRC to generate ranked candidate annotations for LC-MS AIF features, when you need to confirm that (1) the top-ranked candidate match is chemically…
Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format) from a bacterial or fungal strain and corresponding genomic sequence data (FASTA, antiSMASH .final.gbk, or…
Use when when you have predicted retention times from a DNN model trained on one chromatographic method (CM) and need to rank or filter metabolite candidates on a different…
Use when you have LC- or GC-HRMS data in mzML format and a feature list (CSV/TSL/Excel) from external feature detection software (e.
Use when you have a trained NeatMS neural network model (.h5 format) and need to select an operating threshold for peak classification on your LCMS dataset.
Use when you have a Mass Spectrum Point (MSP) file containing electron ionization mass spectral records with header fields and peak intensity pairs, and you need to load it into…