Use when analyzing CE-MS(/MS) data where electroosmotic flow fluctuations cause variable migration times for the same compounds across runs.
Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is…
Use when you have located a workflow definition file (YAML or JSON) in a versioned release or commit and need to verify that it conforms to the schema specification for that…
Use when when processing LC-MS mass tracks (EICs) and you need to identify genuine chromatographic peaks rather than noise artifacts.
Use when when you need to programmatically interface with a TensorFlow Serving model instance and must discover or validate the expected input names (e.
Use when preparing labeled LC-MS peak data for neural network training and you need to decide whether class imbalance in your dataset should be preserved or corrected in batch…
Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to…
Use when when you have multiple file format variants (compressed indexed gzip, standard gzip, SQLite database, uncompressed mzML) that all need to be read via a unified interface,…
Use when you are preparing to run a complex multi-tool bioinformatics pipeline (such as HiC-Pro) on a new system or cluster, and need to confirm that all required binaries exist…
Use when you have identified a claim that one tool outperforms another (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms') in a research article's abstract or introduction, but the…
Use when you have calibrated m/z peak lists, configured adduct transformations (e.g., [M+H]+, [M+Na]+, [M-H]−), and need to annotate peaks with molecular formulae from KEGG,…
Use when when you have sampled the feasible flux solution space of constraint-based metabolic models (via optGpSampler or equivalent uniform sampling) and need to normalize flux…
Use when you have tandem mass spectra with precursor m/z and observed fragment peak m/z values (as mz/intensity pairs), and you need to construct interpretable feature vectors…
Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with…
Use when you have cloned a scientific repository containing Python code (scripts, Jupyter notebooks, or module imports) and need to execute it locally or on new hardware.
Use when you have a mass spectral library (EI or MS2 format) loaded into R via read_lib() and possess either MOL files (from Lib2NIST export) or an SDF file containing the…
Use when you have MS/MS spectra with fragment frequency annotations (from consensus spectrum generation) and need to decide which fragments to retain versus remove.
Use when after installing ENPKG or any component of the workflow via conda/pip dependency manifests and before executing workflow scripts.
Use when you have MS2 spectral data (precursor m/z, retention time, and fragment ion patterns) from UPLC-HRMS analysis of environmental or biological samples and need to assign…
Use when when you have a web-based visualization of aligned mass spectrometry peaks (m/z, intensity, retention time, alignment quality metrics) and need users to interactively…
Use when after installing R or modifying an R environment via conda, package managers, or container images; before running any pipeline step that depends on R packages for…
Use when when you have preprocessed MS/MS spectra converted to a bag-of-fragments
Use when when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) that must be fed into a CNN model for metabolite annotation…
Use when after chromatographic peak detection on preprocessed LC-MS data when you have an xcms result object (XcmsExperiment or xcmsSet) with detected peaks and need to collapse…
Use when you have genomic clusters (GCFs) and metabolomic features (MFs) from paired microbial datasets, each with strain membership information, and you need to score potential…
Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5)
Use when when you need to evaluate GNN performance on collision cross section prediction using the enveda/ccs-prediction repository, either by loading an existing pre-trained…
Use when you have completed cluster-based filtering of KEGG candidate assignments in untargeted LC-MS metabolomics and need to rank those candidates by biological plausibility…
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 you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) and need to convert them into normalized, queryable spectral objects for downstream anal — from…
Use when when working with raw 1H NMR FID data acquired on instruments like Bruker Avance spectrometers that require baseline correction, phase adjustment, and signal alignment…
Use when you have a validated ReDU sample-information metadata table (gnps_metadata.tsv) loaded from a MassIVE accession, and you need to partition public MS/MS files into…
Use when you have defined a Keras model architecture (convolutional and dense layers) accepting raw mass spectrometry imaging data tensors and need to prepare it for training on…
Use when you have variable-length lists of MS/MS peaks (m/z and intensity pairs) that need to be encoded into a fixed-dimensional representation compatible with transformer…
Use when you have preprocessed tandem mass spectrometry spectra converted into a bag-of-fragments representation (with fragments and neutral losses extracted and noise filtered)…
Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a…
Use when you have labeled training data (e.g., pqm_development with 500 peaks and 89 samples) and need to select which of multiple classification algorithms (e.g., AdaBoost,…
Use when when you have Rust source code (such as the mzPeak format implementation
Use when after completing sample alignment in JPA (Part 5) or when ingesting a peaklist or aligned feature matrix from prior peak-picking runs, parse feature metadata to enable…
Use when you have a small training dataset for molecular property prediction (e.g., <500 samples from PredRet or MoNA databases) and a pre-trained GNN model is available that was…
Use when you have a Docker image published to a registry (e.g., docker://stravsm/msnovelist6),
Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's…
Use when you have preprocessed MS/MS spectral data (converted to bag-of-fragments
Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.
Use when you have raw MS/MS feature data with m/z, retention time, and fragmentation spectra from an untargeted metabolomics experiment, and you need to annotate reaction-derived…
Use when you have generated gene-level count matrices via two methodologically distinct routes—e.
Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to…
Use when you have log2-transformed, standardized peak intensity matrices with metabolite annotations (peak ID → KEGG/ChEBI IDs) and need to test whether groups of peaks co-vary…
Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a…
Use when you have run a peak-calling algorithm on sparse CUT&RUN bedGraph data and received a BED-format output file;
Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired from a multiplexed (interleaved) ion mobility experiment, and you need to recover indivi — from…
Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the…
Use when after anchor feature pairs (m/z and retention time values) have been selected from two disparately-acquired LC-MS datasets, and you need to correct for systematic…
Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata…
Use when you have NMR-based metabolomics measurements from a cohort containing both plasma and serum samples with associated processing delay metadata (pre- and…
Use when you have multiple MS/MS spectra (replicates) for a single metabolic feature (same m/z and RT window) and need to identify which fragments are reproducibly detected across…
Use when you have a CSV or Excel file containing chemical structure descriptors for one or more molecules, and you want to obtain binary bitter/not-bitter predictions for each…
Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final…
Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
Use when you have raw LC/MS data in mzML format and need to execute a complete non-targeted screening workflow to extract and annotate chemical features.