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 you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.
Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf,…
Use when you have a compiled EI or MS2 library object (read from MSP format via read_lib) and access to NIST ri.dat and USER.DBU files; you need to populate RI values for…
Use when when ingesting mass spectral libraries (EI or MS2) where SMILES information is embedded in the Comment field rather than in a dedicated SMILES metadata field—particularly…
Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those…
Use when you have multiple MSP or spectral library files (e.g., one per batch of analytical standards, or organized in a directory structure) that need to be read and merged into…
Use when you have loaded an MS2 library (from NIST, GNPS, or other sources via read_lib()) that contains both positive and negative ionization modes mixed in a single file, and…
Use when when evaluating a trained spectral embedding model on publicly available datasets (GNPS, MoNA, MTBLS1572, MassBank, or MassSpecGym) and you need to report averaged…
Use when after harmonizing MS/MS spectra and metadata fields (compound identifiers, adduct annotations, collision energies, instrument types) to a common schema, and before…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single — from…
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 a .msp spectral library file with sparse or incomplete metadata (e.
Use when after loading an MSP spectral library file into memory using mssearchr's MSP parser, when you need to verify that each spectrum record contains complete and valid…
Use when processing a mass spectrometry dataset (in FragHub JSON format or similar) where duplicate spectral records are suspected or known to exist.
Use when when importing mass spectrometry spectral data from public repositories or multi-source MGF/MSP files where metadata fields are inconsistent, missing, or non-standard;
Use when processing heterogeneous mass spectral datasets from multiple open libraries (e.g., MassBank, UNPD, GMD) where structural identifiers, precursor m/z, and adduct…
Use when you have downloaded raw spectroscopic data files (NMR, HSQC, COSY, IR modalities) from the Zenodo repositories and need to convert them into the standardized multi-modal…
Use when you have preprocessed MS/MS spectral data (converted to bag-of-fragments
Use when when you have resolved mzML or mzXML spectrum files and need to isolate signals for a target m/z value (e.g., 870.954) across all retention times or a specific scan.
Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment…
Use when immediately after extracting ion chromatograms (EICs) by binning mass spectral data across the full m/z range from raw LC/HRMS files (mzML, mzXML, or netCDF format).
Use when you have raw MS/MS spectra in multiple formats (.mgf, .msp, .mzML) that contain background noise, instrument artifacts, or low-abundance fragments that would degrade…
Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D…
Use when when comparing two MS/MS spectra where the precursor m/z values differ (indicating potential mass modifications, adducts, or related compounds), and you want to detect…
Use when you have an annotated or raw tandem mass spectrometry spectrum and need to identify which observed peaks correspond to expected peptide fragment ions from a known or…
Use when you have raw MS/MS spectra with variable numbers of peaks at continuous m/z values and need to feed them to a neural network (e.g., Siamese network for similarity…
Use when after peak detection on individual GC-IMS samples, when you need to assign consistent cluster IDs to peaks detected across multiple samples to enable cross-sample…
Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or…
Use when you have raw LC-MS data in mzML or mzXML format and need to extract reproducible, high-quality metabolite features (m/z, retention time, intensity) for global…
Use when you have raw INADEQUATE NMR spectra files and need to transition from continuous spectral data to discrete peak coordinates.
Use when when you have aligned mass tracks (extracted ion chromatograms) across multiple LC-MS samples consolidated into a composite map and need to detect reproducible elution…
Use when when you have variable-length MS/MS peak lists (m/z and intensity arrays) that must be fed into a transformer-based model for spectra analysis, and you need…
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 working with raw or minimally processed MS/MS spectra from repositories
Use when you have raw or annotated MS/MS spectra (in MGF, mzML, or mzXML format) destined for de novo peptide sequencing with Casanovo.
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 extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument…
Use when you have multiple replicate MS/MS spectra for the same metabolic feature (e.g., 66 top-TIC spectra for feature 1982) and need to identify robust peaks by merging nearby…
Use when raw Agilent MassHunter (.d) or UIMF mass spectrometry files exhibit jagged or noisy peaks, particularly for low-abundance ions where signal-to-noise ratio is poor.
Use when when you have MS/MS spectra (LC-MS or equivalent positive ionization mode data) that you intend to embed using Word2Vec or similar distributional semantic models, or when…
Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry
Use when when preparing raw MS2 spectra (m/z and intensity pairs) for kernel-based scoring methods such as IOKR, especially when the training dataset is large and represents…
Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment…
Use when you have a query mass spectrum (or representative metabolite spectrum from public data) and need to identify it by searching against large spectral reference databases…
Use when after running annotateRC to generate ranked candidate annotations for LC-MS AIF features, when you need to confirm that (1) the top-ranked candidate match is chemically…
Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by…
Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format)…
Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
Use when when you have processed LC-MS/MS spectral data in .mgf format with feature identifiers and need to compute a pairwise similarity matrix to support interactive exploration.
Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and…
Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a…
Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g.,…
Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from…
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 you have a query electron ionization (EI) mass spectrum and need to search it against a library of known EI mass spectra to identify unknown compounds.
Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT.
Before dispatching a multi-agent team, run a spectral diagnostic on the proposed communication graph and emit a (ρ, Δ, κ) coordination signature plus a pass/fail verdict against…
Use when when you have a collection of MS/MS reference spectra and unknown query spectra that must be rapidly matched against a large spectral library, and you need to enable…
Use when rendering the Next Steps footer after any spectre command, suggesting next actions, or when users need guidance on which SPECTRE command to run.