Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or…
Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
Use when after retention-time-based and abundance-correlation-based feature grouping have produced composite feature groups, and you need to identify which features within a group…
Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly…
Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL…
Use when you have raw or processed MS spectrum data (m/z and intensity pairs) from DI-MS, ASAP-MS, or other high-throughput mass spectrometry instruments that requires automated…
Use when you have GC-MS data with multiple replicate injections or samples, need to identify a predefined set of query chemicals by name, and want to consolidate all instances of…
Use when you have trained or loaded a deep learning model that produces high-dimensional spectral embeddings (e.g., 200-dimensional vectors from MS2DeepScore base network) and…
Use when after log-transformation and missing-value imputation of a metabolomics
Use when you have RNA-seq read count data and a metabolic model with GPR rules, and you need to assess how differential gene expression translates into differential metabolic…
Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON…
Use when when you have a pre-trained encoder (e.g., TCN spectrum encoder in FIDDLE) that has learned useful representations on a source task (e.g., MS/MS spectrum encoding), and…
Use when after applying CordBat batch correction to a log2-transformed metabolite matrix from multi-batch metabolomics data, you want to quantitatively and visually assess whether…
Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
Use when you have a preprocessed feature table from non-targeted LC-MS/MS metabolomics data (after data merging, cleanup, blank removal, and batch correction) and need to test…
Use when you have a txt or tabular export file from a liquid chromatography–mass
Use when you have raw mass-spectrometry files (MGF, BIOM, mzXML, mzML) or feature abundance tables from external tools (MZmine2, peak detection software) and need to convert them…
Use when when you have computed pairwise distances between MS2 fingerprint vectors from multiple metabolomics samples and need to visualize sample similarity relationships in low…
Use when after differential peak analysis (tl.diff_test) has identified peaks that differ in accessibility across cell types or conditions.
Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to…
Use when you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values…
Use when when processing LC-MS mass tracks (EICs) and you need to identify genuine chromatographic peaks rather than noise artifacts.
Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their…
Use when after running GNPS molecular networking, SIRIUS compound identification,
Use when you have retrieved a complete set of project JSON documents from a data platform and need to verify that each document's structure, field types, and required properties…
Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
Use when apply this filter after loading raw .idat files or beta-valued matrices from HumanMethylation450 or EPIC methylation arrays when you need to remove probes with…
Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to…
Use when when you have prediction scores (softmax probabilities, uncertainties) from a trained deep learning model evaluated on a heterogeneous dataset and you need to determine…
Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS…
Use when after individual mass tracks (EICs) have been extracted from each sample''s mzML file and you need to create a unified, cross-sample m/z reference structure.
Use when you have a Sphinx-based documentation project with multiple gallery scripts (e.
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 after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table…
Use when you have raw mass spectrometry instrument output (mzML, vendor binary formats, or mzPeak archives) and need to load spectrum metadata, chromatogram data, or signal arrays…
Use when after peak detection in a nontargeted LC-MS workflow when you have a feature table with detected peaks and need to filter low-quality features or understand why certain…
Use when you have measured intracellular metabolite concentrations (e.g., via LC–MS/MS) across multiple cell lines or samples and want to predict which metabolic reactions are…
Use when you have an unknown MS/MS query spectrum with a known or measured precursor m/z value and need to search a spectral library (local or public: GNPS, MASSBANK, DrugBANK) to…
Use when you have XCMS-processed LC/MS peak data from dual-labeled (e.g., 13C) and unlabeled (12C) metabolomics samples and need to distinguish features genuinely enriched by…
Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both…
Use when you have a GNPS-generated molecular network (either classical or feature-based) and corresponding MS2LDA experiment output containing Mass2Motif-to-spectrum assignments,…
Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type…
Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix.
Use when you have raw CE-MS data and need to (1) transform migration time values to effective mobility using two calibration markers (e.
Use when you have isotope-corrected or raw ion-image intensity matrices from LipidQMap or similar MSI software and need to: (1) export them as persistent HDF5 containers for…
Use when after executing a molecular networking workflow on GC-MS data that has been processed through auto-deconvolution, and a published reference network exists from a prior…
Use when when you have partitioned public MS/MS files from MassIVE using the ReDU File Selector into one or more filtered groups (G1–G6) and need to verify that each group's file…
Use when you have execution-time metrics (from a benchmark table or profiling logs) across multiple visualization backends for the same set of plots (e.
Use when you have collected liquid chromatography (LC) spectra and retention time labels for your in-house molecular database, and you want to leverage a pretrained GNN-RT model…
Use when when implementing or extending a DSL parser (lexer + recursive descent or LALR parser) that accepts user-authored query strings.
Use when when you have loaded both a known compound and its modified analog with MS/MS spectra, initially generated baseline modification probability scores, and then obtained or…
Use when you have a query mass spectrum and a set of candidate molecular structures, and you need to prioritize candidates by their likelihood of matching the query.
Use when your CE-MS dataset exhibits migration time drift between runs due to electroosmotic flow (EOF) variation, and you have identified two internal mobility markers (e.g.,…
Use when when you need to confirm that a Java project's GitHub Actions workflow (e.g., 'dev_build_release.yml') has completed successfully and generated usable build artifacts;
Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays
Use when you have Spectra objects in an R environment and need to apply Python MS algorithms (e.g., matchms similarity scoring, spectrum normalization, or filtering) that operate…
Use when you have transcript-level abundance, count, and length estimates (from salmon, Sailfish, or kallisto via tximport) and want to perform gene-level differential expression…
Use when after preprocessing GCxGC-MS chromatograms (smoothing, baseline correction, peak alignment) when you need to uncover latent metabolite patterns that distinguish…
Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.
Use when when you have a set of molecules with known chemical structures and need to prepare them for classification or prediction tasks.