Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
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 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 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its…
Use when you have IM-MS measurements of samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract) and need to assess whether measured CCS values…
Use when when building reproducible Python-based computational workflows that must serve both beginner and expert users; when the analysis requires interactive parameter tuning,…
Use when you have measured IM-MS lipidomics data spiked with U13C labeled internal standards and need to assess whether CCS bias remains within acceptable limits for each lipid…
Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
Use when your IM-MS lipidomics samples have been spiked with fully labeled isotopic internal standards (e.
Use when you observe jagged or noisy peak profiles in low-abundance ions after loading raw IM-MS data (Agilent MassHunter .
Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce…
Use when after completing an Environment simulation or replay with scan-level MS2 acquisition control, and evaluation data has been collected in memory.
Use when augmenting mass spectrometry ion images for contrastive learning, specifically when you need to simulate the natural Poisson noise that arises from photon-counting…
Use when when you have raw profile LC-MS data in .mzML format and need to prepare regions of interest (ROI) as input for a CNN-Transformer peak detection network.
Use when when you have extracted feature tables from multiple breath samples (mzML/mzXML files) using feature extraction, and you need to identify which features are the same…
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 ingesting or validating project JSON documents against a schema (such as app/public/schema.json in the Pairing Omics Data Platform) that designates certain fields as URL…
Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root…
Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of…
Use when you have custom lipid species (not covered by the 500,000+ built-in LipidMatch entries) that you need to match against experimental MS/MS data, or you are extending…
Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend.
Use when you have implemented or are evaluating an algorithmic or system optimization (e.g., MASST+) that claims to reduce execution time, and you need to quantify and…
Use when after peak detection and feature extraction have produced a composite feature table with m/z, retention time, and intensity values for individual samples.
Use when you have raw or curated mass spectrometry data (MS1, MS2, or MSMS) in mzML, mzXML, CDF, MGF, MSP formats, or from a MassBank/MetaboLights repository, and need to convert…
Use when a user submits one or more MS/MS spectra (via .mgf file, USI list, or direct upload) and the downstream analysis requires dispatching to a specific domain-specific MASST…
Use when you have extracted retention times from MS1 spectra for top signals in a single LC-MS/MS run and need to evaluate whether that gradient's separation performance is…
Use when when processing aligned LC-MS data across multiple samples where the computational bottleneck is repeated peak-detection algorithm calls (one per sample per m/z value).
Use when after XCMS feature detection, grouping, retention time correction, and missing value filling have produced an aligned feature matrix, when you need to group features…
Use when you have computed raw strain correlation scores (based on shared strain membership) between genomic and metabolomic objects of heterogeneous sizes, and you need to…
Use when you are selecting a pathway enrichment method for metabolomics peak data and need to assess which method will remain stable when your data contains noise, dropout, or…
Use when you have 1D or 2D NMR spectra (1H and/or 13C) and need to predict unknown molecular structure (formula and connectivity) up to ~19 heavy atoms; or you have a set of…
Use when you have consensus metabolic reconstructions for multiple community members (e.g., plant-associated microbes or plant-microbial consortia) and those individual models…
Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool.
Use when when beginning a MEMO analysis workflow with raw or unaligned MS2 spectra files and needing to extract fragmentation data and precursor information before counting MS2…
Use when after clustering features with RAMClustR and inferring molecular weights via do.findmain, when you need to perform structure elucidation or molecular formula prediction…
Use when you have processed MSI peak data (in rMSIproc format) and need to distinguish matrix-related ions from analyte signals.
Use when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC bedGraph format…
Use when you have transcript-level abundance estimates (from Salmon, kallisto, or similar) and a set of defined alternative splicing events (in ioe or ioi format), and you need to…
Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your…
Use when you have a compressed mzML file (mzML.gz or indexed gzip format) and need to extract a single spectrum or a small subset of spectra by their known numeric identifiers,…
Use when when you need to reproduce a computational workflow described in a GitHub repository, validate CI/CD pipeline definitions (e.g., GitHub Actions workflows), inspect source…
Use when when you have a feature abundance table (rows=features, columns=samples)
Use when after loading raw metabolomics data (e.g., from Metabolon, Nightingale,
Use when you have MSBERT-preprocessed spectral datasets (GNPS, MoNA, or MTBLS1572 format) with SMILES annotations before training a spectral embedding or compound identification…
Use when when ingesting or updating MassBank records in plain-text or structured format, and you need to verify that metadata fields (accession, name, formula, mass, spectrum…
Use when you have a heterogeneous feature matrix combining molecular descriptors (from RDKit/mordred) and chromatographic metadata (column length, temperature, pH, flow rate,…
Use when you have a list of candidate metabolites for an unknown compound (from mass-to-structure search or library matching), experimental retention time(s) from one or more…
Use when after organism name cleaning and taxonomy verification (4_cleaningTaxonomy.R) have been completed and you have a cleaned organism table with standardized names.
Use when you have extracted clustering or classification accuracy metrics (NMI, ARI, purity scores) for two or more competing methods evaluated on multiple datasets, and need to…
Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and…
Use when when you need to verify that a research software package (e.g., MassQL) maintains functional correctness over time, assess the reliability of a tool before integration…
Use when when you have mass spectrometry imaging root datasets paired with accompanying .mat workspace files (as in the B73 and Oaxacan Green genotypes from Sama et al.
Use when when XCMS-aligned LC-MS data shows coefficient of variation (CV) above expected thresholds for known features, or when analyzing long-duration experiments (>1 week) or…
Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites…
Use when before initiating raw file conversion or feature extraction, when you have a heterogeneous collection of raw LC-MS files (.raw or .mzML) and sample information scattered…
Use when after rMSIcleanup has classified ions as matrix-related or non-matrix, and you need to audit, validate, or communicate the annotation decisions.
Use when training a CNN model from scratch on LCMS peak classification tasks (or similar image-like batched data) where you need to confirm the model reaches target performance…
Use when you have raw MS intensity data paired with known-concentration calibration standard measurements, and you need to convert intensities to absolute or relative…
Use when after retrieving a JSON or tabular response from a web service endpoint (such as CANOPUS), validate the result before parsing or integrating it into your analysis…
Use when when you have constructed a MassGrid (m/z-aligned mass tracks across multiple samples) and need to retrieve all sample-specific mass tracks for a given m/z value in order…