Use when you have a query spectrum (or set of query spectra) and need to rank candidate library spectra by their likelihood of sharing the same chemical structure.
Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational…
Use when after computeDeviations has generated a SummarizedExperiment object with z-score assays reflecting bias-corrected deviations of observed vs.
Use when when you have modifications to propose for a shared codebase (e.g., bug fixes, new features, or documentation updates) and need to integrate them without disrupting the…
Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time…
Use when you have executed a complex multi-step processing pipeline (e.g., ENCODE Hi-C uniform processing pipeline) and need to confirm that the generated output files match a…
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 starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z,…
Use when when loading MS/MS spectra from MGF files for FIDDLE model training or evaluation, or when preparing spectrum–annotation pairs for rescore model data augmentation (TCN…
Use when you have a filtered set of conformers (100s–1000s) from ASE-ANI that each require independent quantum calculations via QUICK, and you have access to HPC resources with…
Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential…
Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST tools and need to synthesize results across domains (e.
Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct…
Use when when you need to generate a realistic LC/GC-MS feature table (peak intensity matrix) with controlled, quantifiable condition effects (e.g., differential metabolite…
Use when when a software project has reached a stable milestone (v-tagged commit) and you need to produce official distribution artifacts with verified version metadata,…
Use when when implementing or auditing a deep learning pipeline for MS/MS-based molecular formula prediction, verify that precursor m/z values in the input feature array are…
Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train an interpretable model (e. — from HolobiomicsLab/asb-skill-collections
Use when you have two or more independently processed MemoMatrix objects (each generated from a separate sample set) and your analysis goal requires direct comparison of MS2…
Use when after feature detection when you have a feature table with m/z, retention time, and intensity columns, and you need to group features into empirical compounds (putative…
Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments…
Use when after peak picking (e.g., via MS-DIAL) and quality control filtering, when you have a raw feature abundance matrix with intensity values across multiple samples and need…
Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or…
Use when you have QCpool (pooled quality control) samples measured at regular intervals across one or more LC-MS/MS sequences and need to detect whether instrument performance…
Use when you have molecular descriptors or fingerprints for a set of compounds (e.g., from LC-MS metabolomics) and need to predict a continuous property—such as HPLC retention…
Use when you have integrated, normalized lipidomic and metabolomic feature tables from the Multi-ABLE method or similar concurrent multiomics workflows, with matched sample…
Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z…
Use when when you have imported raw mass spectrometry spectral data (in formats like mzML, mzXML, msp, MGF, or JSON) and need to clean peak lists before metadata validation,…
Use when you have multiple independent implementations of the same data format reader (e.g., Rust, Python, R versions) and need to verify they produce identical or equivalent…
Use when you have sampled flux distributions from two or more constraint-based metabolic models representing different biological conditions (e.
Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers,…
Use when after extracting raw MS/MS spectra from mzML files but before consensus spectrum generation, when you observe high-resolution fragment lists where nearby peaks (within a…
Use when after peak detection when you have a table of detected peaks with m/z values and need to improve mass accuracy for downstream annotation.
Use when after creating a fresh conda environment from a pinned dependency specification (environment.yml or requirements.txt) and installing packages via conda and/or pip.
Use when after generating raw Hi-C contact matrices from aligned reads (post-merge, pre-analysis).
Use when you have raw LC-MS data in vendor or mzML format and need to systematically discover and extract all detectable metabolite features across the full retention time range,…
Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) from one or more metabolomics samples, and you need to prepare them for MS2 fingerprint — from…
Use when your Hi-C data is stored in cooler format (a binary HDF5-based sparse matrix with associated genomic bins and genomic tracks); you need to programmatically access the…
Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
Use when when setting up imzML Writer for the first time on a new machine, or when raw vendor mass spectrometry file conversion fails with ''msconvert not found'' or Docker image…
Use when when you have a containerized scientific tool available on Docker Hub (e.
Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT.
Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected)
Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for…
Use when after loading an MS-DIAL feature table when you need to separate features into two disjoint groups: one meeting a quantitative threshold (e.g., m/z decimal values outside…
Use when you have an experimental MS/MS spectrum (m/z and intensity pairs in mzML/mzXML format from DDA or targeted acquisition on Thermo, Waters, or Bruker instruments) and need…
Use when after network partitioning, when you have identified connected subnetworks of features matched by isotope or adduct patterns and need to sanitize and categorize the…
Use when you have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z…
Use when when performing gene-level differential expression analysis on RNA-seq data where samples may express different isoforms of the same gene at different relative…
Use when when you have a peptide sequence and need to predict which fragment ions (B and Y series) should appear in an MS2 spectrum at a known isotopic abundance (e.g., natural…
Use when when you have CE-MS raw data (mzML or netCDF format) with extracted ion traces for target compounds and need to identify peak boundaries and extract quantitative peak…
Use when you have computed pairwise similarity or mass difference scores between all fragment ions across two tandem mass spectra and need to select the non-overlapping set of ion…
Use when after applying mspcompiler pipeline transformation steps (e.g., reorganize_mona, assign_smiles, assign_ri, read_multilibs, separate_polarity, complete_mgf) to confirm the…
Use when you have paired predicted and observed metabolite abundance vectors from a predictive model (e.
Use when when you have computed Reaction Activity Scores (RAS) from transcriptomics and GPR rules, Reaction Presence Scores (RPS) from RAS normalized flux predictions, and Flux…
Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and…
Use when you have completed cross-validation tuning of one or more machine-learning
Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation…
Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak…