Data
pyopenms-skill
Handle computational mass spectrometry workflows with PyOpenMS: read and write mzML/mzXML/MGF files, execute signal processing steps such as smoothing and peak detection, identify …
Research
bio-metabolomics-isotope-tracing
Designs and interprets stable-isotope tracing experiments (SIRM/fluxomics) using 13C/15N/2H tracers to measure metabolic activity. Handles tracer selection, isotopologue distributi…
Data
spectral-entropy-quality-assessment
Filters and ranks metabolite annotation candidates in untargeted MS workflows by spectral quality after feature detection and alignment. Combines fragmentation similarity scores wi…
Data
fragmentation-spectrum-extraction
Use when you have raw or peak-detected mass spectrometry data (mzXML, mzML, or netCDF format) from untargeted metabolomics or exposomics studies and need to separate composite frag…
Data
multi-assay-data-integration-and-harmonization
Integrates multiple independent LC-MS assays (e.g., positive/negative ionization, varied lipid or chromatographic methods) from the same cohort into unified discriminant or regress…
Data
principal-component-extraction-from-pathway-subsets
Compute a single activity score per pathway from a log2-normalized, zero-mean, unit-variance metabolite intensity matrix by extracting the principal component that captures coordin…
Data
bio-proteomics-metabolomics
Workflow skill for proteomics, metabolomics, lipidomics, and mass spectrometry data including mzML/mzXML processing, DDA/DIA analysis, peptide identification, protein inference, PT…
Data
coefficient-of-variation-comparison
Filters metabolomic features by comparing coefficient of variation between QC replicates and study samples, removing those with unstable or poorly reproducible signals after normal…
Data
mzml-metabolomics-data-import
Handles import and initial processing of LC-HRMS metabolomics data from mzML or ABF files, supporting reproducible pipelines for public or proprietary datasets from repositories su…
Data
nontargeted-analysis-workflow-execution
Execute nontargeted analysis on UPLC-HRMS data from any vendor (ThermoFisher, Agilent, others) after MSConvert conversion, feeding batch files into MSThunder for deep learning stru…
Data
eic-signal-peak-detection
Detects and quantifies discrete peaks in EIC chromatographic profiles from LC/HRMS data (mzXML, mzML, netCDF), returning retention times, apex intensities, and quality metrics for …
Data
spectral-data-object-construction-and-integration
Constructs integrated spectral data objects from centroided mzML files for targeted metabolomics and lipidomics, enabling polarity filtering, QC stratification, and batch-aware pea…
Data
metabolite-abundance-normalization-across-conditions
Normalizes intracellular metabolomics abundance data from multiple replicates across cell lines or conditions into a unified, comparable metabolite dataset ready for downstream ana…
Data
matchms
Process and compare mass spectrometry data from mzML, MGF, and MSP files; compute spectral similarity (cosine, modified cosine), harmonize metadata, and support compound identifica…
Data
statistical-distribution-visualization
Generates visualizations of statistical distributions (means, medians, standard deviations, frequencies) from computed molecular fingerprints or feature vectors to validate expecte…
Research
feasible-flux-distribution-sampling
Sample feasible flux distributions in cell-relative metabolic models after integrating transcriptomics, metabolomics, and extracellular constraints to visualize and compare metabol…
Data
json-spectral-data-processing
Processes mass spectrometry spectral data in JSON, CSV, MSP, or MGF formats: standardizes field names, validates chemical identifiers (SMILES, InChI, InChIKey), removes duplicates,…
AI / ML
spectral-embedding-extraction-from-neural-networks
Extracts 200-dimensional spectral embeddings from binned, square-root-transformed MS/MS spectra using a trained MS2DeepScore Siamese network for clustering, chemical space mapping,…
AI / ML
ion-mobility-machine-learning-training
Train ML models on molecular structures or descriptors paired with collision cross section data to predict CCS values for up to 10,000 new molecules, supporting metabolomics identi…
AI / ML
spectral-embedding-generation
Generates spectral embeddings from pre-processed, normalized MS/MS spectra using a trained MS2DeepScore network for pairwise structural similarity or chemical-space visualization v…
Data
distance-metric-calculation-bray-curtis-euclidean-jaccard
Calculates Bray-Curtis, Euclidean, and Jaccard distances on normalized metabolomics peak data or presence/absence matrices to quantify sample-to-sample compositional differences be…
Data
molecular-networking-construction
Builds molecular networks from LC-MS/MS DDA data by clustering fragmentation spectra on similarity, enabling metabolite annotation, cross-sample comparisons, and discovery of struc…
Data
alterlab-metabolomics-wb
Query the NIH Metabolomics Workbench REST API for 4,200+ studies, metabolites, RefMet nomenclature, MS/NMR spectra, m/z searches, and metadata. Supports biomarker discovery and met…
Data
bio-multiomics-systems-biology
Integrates multi-omics datasets (transcriptome, proteome, metabolome) with pathway enrichment, network analysis, and constraint-based metabolic modeling using tools like MOFA, GSEA…
Data
chromatographic-peak-quality-metric-evaluation
Evaluates peak integration quality in untargeted LC-MS metabolomics data processed with XCMS, flagging low-quality integrations that could add noise or bias to compound identificat…
Data
cosine-similarity-computation
Computes cosine similarity between two MS/MS spectra to quantify resemblance for compound identification or molecular networking, using a symmetric measure unaffected by precursor …
Data
single-cell-spatial-metabolomics-data-processing
Aligns IMC and SIMS imaging from identical tissue sections via spatial registration, cell segmentation, and per-cell extraction of protein and metabolite intensity profiles for joi…
Data
metabolomics-feature-integration-assessment
Assesses peak integration quality in XCMS-processed metabolomics data, identifying low-quality or unreliable features in xcmsEIC and filled xcmsSet objects before downstream statis…
Research
metabolic-regulation-classification-scheme
Classifies metabolic regulation using Reaction Activity Scores from transcriptomics, Reaction Presence Scores, and Flux Fold-change Distributions derived from metabolomics and mass…
Data
tooluniverse-metabolomics
Identify metabolites and retrieve metabolomics study data from HMDB, MetaboLights, Metabolomics Workbench, and PubChem. Supports annotation, pathway lookup, and report generation f…
Data
hmdb-formula-sampling
Generates diverse in silico LC-MS/MS datasets from HMDB entries that match real metabolomic chemical backgrounds, for testing fragmentation methods or acquisition logic within a sp…
Data
sample-replicate-pair-assessment
Identifies reproducible feature pairs across biological replicates when given high-throughput measurements such as mass spectrometry metabolomics, applying a user-defined reproduci…
Data
spectral-library-matching
Match MS/MS spectra in .mgf or USI format against curated reference libraries to identify unknowns, assign Level 2 metabolomics annotations via GNPS, and aggregate results across o…
Data
metabolite-spectral-data-merging
Merges multiple mass spectral libraries from varied formats (NIST MSP, MoNA, GNPS MGF, RIKEN) into a unified collection with harmonized metadata including SMILES, InChIKey, and mol…
Data
metabolomic-signal-quantification
Extracts quantified feature matrices from raw untargeted LC/MS data in mzML or mzXML format, identifying m/z and retention time features with sample intensities when signal paramet…
Data
multiple-testing-correction-metabolomics
Applies multiple-testing correction to raw p-values from metabolite-phenotype correlations in SummarizedExperiment objects, supporting FDR or Bonferroni adjustment for high-dimensi…
Data
tooluniverse-metabolomics-analysis
Analyze metabolomics datasets from LC-MS, GC-MS, and NMR experiments. Performs normalization, statistical testing, pathway enrichment, and biomarker discovery with multi-omics inte…
Data
hmdb-database
Access the Human Metabolome Database (220K+ metabolites). Search by name, ID, or structure to retrieve chemical properties, biomarker data, NMR/MS spectra, and pathways for metabol…
Data
peak-picking-avoidance-ms-analysis
Analyzes raw 2D mass spectrometry data (m/z vs. retention time) without conventional peak picking, enabling sensitive marker detection at trace levels in untargeted metabolomics an…
Data
hierarchical-clustering-parameter-optimization
Optimizes hierarchical clustering parameters for GC-IMS peak grouping, evaluating Euclidean distance suitability on drift/retention time coordinates and validating dt_cluster_sprea…
Data
fatty-acyl-chain-variant-identification
Identifies related lipid species sharing the same fatty acyl chain(s) when a top-ranked annotation (e.g., LPC(14:0)) is assigned, checking for lower-scoring spectral matches across…
Data
metabolite-annotation-taxonomic-integration
Integrates taxonomic metadata with metabolomics results to filter candidate annotations, retaining only metabolites consistent with the source organism or tissue and improving rank…
Data
batch-effect-correction-qc-reference
Detects and corrects batch effects in peak intensity matrices using QC reference samples, preserving biological variation while removing technical drift in retention time and signa…
Data
mass-error-calculation-and-reporting
Calculates and reports mass errors after molecular formula assignment on calibrated m/z data, quantifying formula-to-peak match accuracy and validating calibration against referenc…
Data
targeted-metabolite-extraction
Extracts and quantifies targeted metabolites or lipids from centroided LC-MS (.mzML) files using m/z, retention time, and polarity lists, returning per-run AUC values plus averaged…
AI / ML
domain-specific-masst-api-integration
Integrates MS/MS spectral searches across multiple curated domain-specific databases (microbial, plant, tissue, microbiome, food) and aggregates, compares, and visualizes matches i…
Research
full-scan-acquisition-strategy
Assesses MS1 ionization efficiency, peak detection sensitivity, and chromatographic separation using full-scan acquisition without MS/MS fragmentation for benchmarking across diver…
Data
chemodiversity-metric-calculation
Calculates chemodiversity metrics from sum-normalized FT-ICR MS peak-abundance matrices with assigned molecular formulas, enabling comparison of metabolite diversity across treatme…
Data
multiplexed-spectrum-decomposition
Handles SWATH-MS data (mzML or vendor formats) containing multiplexed spectra from overlapping precursor windows, enabling decomposition of mixed fragment ions for metabolite ident…
Data
xcms-object-handling-and-preprocessing
Process raw chromatography–mass spectrometry files (NetCDF, mzML) to detect features, align retention times and m/z values, correct drift, and impute missing entries for metabolite…
Data
feature-consolidation-across-batches
Aligns and merges multiple CSV feature tables from separate metabolomic runs into a unified feature-by-sample matrix by matching mass, retention time, intensity, isotope, and adduc…
Data
mass-error-tolerance-filtering
Controls m/z matching stringency when annotating full-scan MS or imaging data against metabolite databases, letting you tune ppm tolerance to balance annotation sensitivity and spe…
Data
permanova-effect-size-interpretation
Interprets PERMANOVA effect sizes on high-dimensional compositional data such as FT-ICR MS metabolite profiles when ordination plots show weak group separation despite significant …
Data
quantitative-mode-metabolomics-configuration
Prepares multi-study metabolomics results—compound IDs, p-values, fold-changes, and sample sizes—for quantitative meta-analysis via weighted Fisher's method and log fold-change agg…
Research
bulk-omics-integrative-planner
Design integrated research plans for bulk transcriptomics, proteomics, metabolomics and related omics from a biomedical direction, defining questions, study patterns, and analysis …
Data
spectral-dataset-partitioning-and-train-test-curation
Creates reproducible train/test splits and uncertainty estimates for spectral libraries when prior boundaries exist, enabling consistent model evaluation across repeated random par…
Data
chromatographic-peak-overlap-resolution
Resolves overlapping chromatographic peaks in GC-MS datasets, enabling accurate compound identification and quantification in complex mixtures from metabolomics or environmental an…
Data
mass-spectrometry-adduct-annotation
Identifies unknown ionization adducts from precursor m/z values in preprocessed MS/MS spectra, supporting metabolomics workflows and de novo formula annotation without spectral lib…
Data
sample-batch-metadata-organization
Organizes tab-delimited metabolomics data into a unified structure for batch correction, handling aliquot IDs, compound names, peak areas, sample types, batch labels, and injection…
Data
biochemical-transformation-matching
Reconstruct biochemical transformation networks from filtered FT-ICR MS peak lists by matching molecular formulas to map microbial and environmental metabolic pathways across condi…
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