Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a…
Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original…
Use when after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
Use when when a tool claims to be 'scalable' or 'performance-conscious' but lacks published performance benchmarks, or when you need to confirm that runtime and memory scale…
Use when after uploading a sample list to InjectionDesign and before performing inter-batch balancing and intra-batch randomization.
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 when you have raw mzML or mzXML mass spectrometry files with uncompressed numeric arrays (not pre-compressed with zlib or msnumpress) and need to reduce file size for…
Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS…
Use when when you need to assess whether a given ATAC-seq clustering method (or variant) is competitive on your data or when evaluating which published method to adopt.
Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic…
Use when you need to validate that Docker image builds for multiple deployment variants (e.g., cli, dev, linux, windows) meet documented compressed size ranges, or when you must…
Use when when you have trained predictive models (e.g., neural networks) on paired microbiome-metabolome data and need to identify which metabolites are genuinely well-predicted…
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 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 when you have generated a scan index from rawrr::readIndex() on a Thermo .
Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly…
Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on — from…
Use when when you have a USI (e.g., mzspec:MTBLS1124:QC07.mzML) pointing to a public mzML or related spectrum file in MetaboLights, MassIVE, or GNPS repositories, and need to load…
Use when when annotating m/z features against a metabolite database (HMDB, Lipidmaps, etc.) and the sample preparation, ionization method, or polarity mode favors specific adduct…
Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/...
Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert each spectrum into a learned molecular embedding — from…
Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage…
Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and…
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 you have LC–MS all-ion fragmentation chromatograms already processed by xcms and clustered by RamClustR, a feature table (targetTable.csv format) listing features to…
Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single…
Use when you have computed raw or standardised correlation scores (or other link-ranking metrics) for all possible GCF-MF pairs in a dataset and want to verify that validated…
Use when you have a peak list extracted from MSI data that includes candidate peaks with potential m/z overlap or spatial co-localization patterns across tissue images.
Use when you have a ranked list of library candidates (top 2000 by MS2Deepscore)
Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar…
Use when when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
Use when you have assembled genome FASTA sequences (from SPAdes, metaSPAdes, or antiSMASH output) and need to systematically identify precursor peptides corresponding to a target…
Use when after extracting NMR spectra and designating replicate QC samples (typically 10 samples run throughout the study), calculate CV for each metabolite feature to assess…
Use when you have merged methylation call data across multiple biological replicates (samples per group ≥2) with base-pair-level coverage information, and you need to identify…
Use when when you have a pre-computed hierarchical dendrogram from structural clustering (e.g., of LC-MS features based on m/z and retention time) and want to compare or validate…
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 beginning preprocessing of a new LC-MS dataset with mzML files or raw acquisitions and you need to determine which ionization mode was used before running feature…
Use when you have acquired raw MS/MS spectra (in MGF or mzML format) from a mass spectrometry instrument or public repository (e.g., MassIVE, MetaboLights, GNPS) that will be used…
Use when you have two peak-picked, conventionally aligned LC-MS metabolomics datasets (e.
Use when you have computed or received a precomputed expected contact frequency table (e.
Use when you have raw .msp spectral library files (e.g., from MassBank or custom sources) and need to convert them into a structured CSV library format for use in metabolite…
Use when you have a combined EI library (from multiple sources such as NIST, RIKEN, MoNA) and access to NIST RI database files (ri.dat and USER.
Use when you have GNPS library accession IDs (e.g. CCMSLIB00011906190) for a reference compound and a chemically or biologically modified analog, and need to load their full MS/MS…
Use when when implementing fragment ion annotation in proteomics workflows and needing to determine whether neutral loss annotation (e.g., H2O: -18.010565, NH3: -17.026549) should…
Use when after loading a feature table into memory when the table contains zero or missing values that represent true signal loss (not genuine absence), and you need to impute…
Use when when you have implemented conditional routing logic in the GNPS_MASST codebase and need to verify that spectrum submissions with explicit domain-context selections (e.
Use when when you have per-feature quality metrics (such as CV values from NMR or MS reproducibility analysis) and need to: (1) confirm that a specified proportion of features…
Use when a practitioner has pre-computed features from an external feature-finding procedure (e.g., vendor software, alternative open-source tools) and wishes to incorporate them…
Use when you have a filtered FT-ICR MS peak list (m/z values and assigned molecular formulas per sample) and wish to reconstruct biochemical transformation networks ab initio to…
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 when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train interpretable machine learning models—particularly decision trees or — from…
Use when when integrating LC-MS/MS data from diverse sources (e.g., public repositories like MSV000080102, instrument outputs, or precomputed workflows) into NPDtools pipelines.
Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
Use when building or maintaining a system that fetches metadata from multiple independent external web services and needs to diagnose why annotation runs fail or slow down.
Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including…
Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass…
Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique…
Use when when you have read LC-MS peak table data from Excel (or equivalent) into R and need to organize it into a structured object that tracks feature abundances, sample…
Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
Use when when you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution.