Use when after retrieving top-scoring library candidates from a full MS2Deepscore comparison, but before or during final re-ranking.
Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
Use when you have LC-HRMS profile-mode data (retention time × m/z matrix format) and need to automatically identify chromatographic peak locations and boundaries prior to feature…
Use when you have uploaded a pre-analytical data table containing sample metadata, processing timestamps (pre- and post-centrifugation), and NMR metabolomic measurements — from…
Use when you have NMR dataset metadata (cache-file flag, total point count, block layout configuration) and need to select an appropriate storage backend that balances memory…
Use when you have an unknown MS/MS spectrum (query spectrum with m/z and intensity pairs) and a reference spectral library (local or public: GNPS, MASSBANK, DrugBANK), and you…
Use when after converting or downloading a pre-trained Keras model to HDF5 TensorFlow 2.3.0 format, particularly when integrating the model into a fixed-interface pipeline (e.g.,…
Use when after converting MS/MS spectra to fixed-length vector representations using a pre-trained Word2Vec model (as in Spec2Vec), filter spectra before computing similarity…
Use when when evaluating a new or updated version of a data processing tool (especially asari or similar LC-MS workflows) before production deployment, or when verifying claims…
Use when after MSConvert has converted vendor-specific raw mass spectrometry data (ThermoFisher, Agilent, or equivalent formats) on a Linux system and before initiating analysis…
Use when a Rust port or alternative implementation of a mapper (e.g., salmon, piscem) consistently maps 2–3% more reads than a C++ reference, especially on short reads.
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 after installing an R package from a non-CRAN repository (such as r-universe) to confirm the package build is sound, dependencies resolve correctly, and no warnings or…
Use when you have a mass spectrum of an unknown metabolite with a known or inferred precursor m/z, you have run a deep-learning semantic similarity model (e.
Use when processing LC-MS/MS data acquired in DDA mode that contains chimeric (co-fragmented) MS/MS spectra—i.e., when a single MS/MS scan contains fragments from multiple…
Use when after quality control, filtering, and normalization of an MS-DIAL-derived
Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test…
Use when you have acquired a mass spectrum from an unknown suspected illicit drug analyte and need to compare it against a synthetic NPS database to rank candidate identities by…
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 when you have executed database search pipelines (Dereplicator, VarQuest, or Dereplicator+) on centroided LC-MS/MS spectra in MGF format and obtained match results with…
Use when after running RAMClustR clustering on XCMS-processed metabolomics data, export spectral data when you need to share clustered spectra with external annotation software…
Use when you have quantification output from two versions or implementations of the same tool (e.g., C++ vs.
Use when you have raw or folded 2D-TIC chromatogram data (typically imported from NetCDF files into RGCxGC chromatogram objects) that exhibits baseline drift, chemical noise, or…
Use when after importing fragment files into AnnData using pp.import_fragments and before performing spectral embedding (tl.spectral) or other dimension reduction.
Use when when you have a complete metabolomics abundance table (e.g., targeted LC/MS or untargeted GC/MS counts) and need to generate synthetic left-censored missingness for…
Use when you have executed batch searches against one or more domain-specific MASST tools and received multiple output files (_microbe.html, _plant.html, _tissue.html,…
Use when you have received paired .imzML (XML metadata) and .ibd (binary data) files from an Imaging Mass Spectrometry instrument and need to discover the imaging geometry, m/z…
Use when you have imported a raw GCxGC-MS chromatogram (NetCDF format folded into 2D-TIC) that exhibits chemical noise, instrumental artifacts, or baseline drift—conditions that…
Use when you have preprocessed metabolomics data stored in a SummarizedExperiment
Use when when you have LC-IM-MS/MS data with measured collision cross section (CCS) values and m/z assignments, and you need to disambiguate sterol isomers (particularly N-Me…
Use when when you have a feature table from LC-MS peak detection (e.g., output from MassCube's nontargeted peak segmentation step) and need to assess which features have adequate…
Use when when building an automated converter discovery and job enumeration system where converter classes are dynamically loaded from package directories and you need to extract…
Use when when running metabologenomic RiPP detection pipelines (MetaMiner) on the same genomic dataset but with different input sequence formats (e.g., contigs.fasta vs.
Use when after fitting candidate GAM splines with B-spline basis functions across a range of basis dimensions (k values 12–20) to anchor feature pairs (m/z and retention time…
Use when you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct…
Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
Use when you have LC-MS/MS data acquired in DDA mode from untargeted metabolomics experiments and need to remove chimeric (co-fragmented) MS/MS spectra that result from multiple…
Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all…
Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization…
Use when you have experimental MS/MS spectra and need to assign definitive molecular identities by matching against a curated spectral library.
Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing…
Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication,…
Use when when you have GC-MS output with Match.Factor values or structural similarity scores from categorate() and need to decide which identified compounds are reliable enough to…
Use when you have acquired high-resolution MS/MS spectra in mzML, mzXML, or MGF format and need to prepare them for large-scale clustering or similarity searching.
Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before…
Use when analyzing CE-MS(/MS) data where electroosmotic flow fluctuations cause variable migration times for the same compounds across runs.
Use when when you have an untargeted metabolomics dataset from HPLC–MS (e.g., mzML, NetCDF) with detected peaks of unknown identity, and you need to disambiguate or validate…
Use when when reading a binary file format with a magic integer or fixed checksum field at a known offset, and endianness is not explicitly declared in file metadata or header…
Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity…
Use when when you have abundance-normalized FT-ICR MS peak data with assigned molecular formulas and need to distinguish between richness (total number of distinct metabolites)…
Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for…
Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks…
Use when when validating a metabolomics pathway analysis method (particularly decomposition-based approaches like PLAGE) against data quality degradation, or when comparing…
Use when you have NMR peak data (1H and 13C chemical shift values) that must be submitted to a remote DeepSAT SMART 3 classification API for structural prediction, and you need to…
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 when you need to verify that a GitHub Actions workflow (e.g., main.yml) executes successfully on your local machine, reproduce a reported passing or failing CI build…
Use when you have raw metabolomics count data (e.g., from mass spectrometry or NMR experiments) in tabular format and associated sample metadata (e.g., treatment groups,…
Use when when annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches…
Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw…
Use when when you have annotated representative LCMS samples (raw mzML files + labeled feature tables in mzmine CSV format) and need to convert them into balanced or unbalanced…