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HolobiomicsLab

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1. ▌
   Multi Dimensional Data Loading And Formatting 2 · holobiomicslab

   Use when you have raw or processed mass spectrometry data in HDF5 (.h5) or mzML format and need to ingest it into DEIMoS for multi-dimensional analysis.
   0 installs
2. ▌
   Targeted Dia Data Extraction From Raw Spectra 2 · holobiomicslab

   Use when when you have raw diaPASEF mzML files, a transition list with target analytes (protein, peptide, charge state), and search results (DIA-NN, OpenSwath output) containing feature metadata (retention time, ion mobility, m/z coordinates), and you need to isolate and visualize signal for.
   0 installs
3. ▌
   Feature Intensity Normalization And Batch Correction 2 · holobiomicslab

   Use when after blank masking and sample dropping, when you have a feature table with intensity values that exhibit systematic variation across sample collection batches or instrument runs.
   0 installs
4. ▌
   Hierarchical Clustering Parameter Optimization 2 · holobiomicslab

   Use when after peak detection in GC-IMS preprocessing, when you need to group peaks across multiple samples and must decide whether euclidean distance is appropriate for your drift time and retention time coordinate space, and when you need to validate that your chosen dt_cluster_spread_ms and.
   0 installs
5. ▌
   Mass Spectrometry Reference Standard Alignment 2 · holobiomicslab

   Use when you have positive- or negative-mode tunemix reference data (with known CCS values, m/z, and measured drift times) and need to establish a calibration model for converting observed drift times into CCS values for downstream feature annotation.
   0 installs
6. ▌
   Multiplexed Spectra Recovery And Deconvolution 3 · holobiomicslab

   Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired from a multiplexed (interleaved) ion mobility experiment, and you need to recover individual, demultiplexed frames to reconstruct conventional IM-MS spectra for downstream omics analysis.
   0 installs
7. ▌
   Peak Map Rendering Retention Time Mz Intensity 2 · holobiomicslab

   Use when when you have loaded mass spectrometry data (from mzML or Bruker .
   0 installs
8. ▌
   Automated Peak Detection Without Conventional Picking 3 · holobiomicslab

   Use when you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak picking algorithms. This is especially valuable when analyzing complex, low-abundance samples (e.
   0 installs
9. ▌
   Ionization Mode Detection From Mass Spectrometry Data 2 · holobiomicslab

   Use when when you have raw LC-MS data in mzML format (converted from .raw or acquired directly in that format) and need to invoke Asari for feature extraction, but the ionization mode is not explicitly specified in your experimental metadata or pipeline configuration.
   0 installs
10. ▌
    Accurate Mass Metabolite Search Against Hmdb 2 · holobiomicslab

    Use when after MS1 feature detection and spectra merging in an untargeted or semi-targeted metabolomics workflow, when you have a list of observed accurate m/z values from high-resolution mass spectrometry (e.
    0 installs
11. ▌
    Marker Feature Identification And Validation 3 · holobiomicslab

    Use when when processing GC–MS or LC–MS data as m/z vs retention time chromatograms and you need to identify biomarker or chemical marker features without conventional peak picking, particularly when false positive detection rates from peak detection algorithms are problematic.
    0 installs
12. ▌
    Quality Control Metric Distribution Analysis 3 · holobiomicslab

    Use when after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
    0 installs
13. ▌
    Chromatographic Peak Detection And Segmentation 3 · holobiomicslab

    Use when you have raw LC-MS data (mzML or vendor format) and need to discover and characterize all chromatographic features present, without prior knowledge of target analytes.
    0 installs
14. ▌
    Collision Cross Section Matching And Annotation 3 · holobiomicslab

    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 derived unsaturated sterols) by matching against a curated database of predicted CCS values and MS/MS fragmentation patterns.
    0 installs
15. ▌
    Collision Energy Optimization For Fragmentation 3 · holobiomicslab

    Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with collision-energy-dependent m/z values and intensities for downstream CCS prediction or LC-IM-MS/MS library matching.
    0 installs
16. ▌
    Mass Spectrometry Imaging Vendor Format Support 2 · holobiomicslab

    Use when your input mass spectrometry imaging data is in a proprietary vendor format (Bruker .d/.baf, or other binary formats not natively supported by MSIGen) and you need to convert it to an open, readable format (mzML or processed binary) compatible with MSIGen's msigen() function.
    0 installs
17. ▌
    Molecular Conformer Generation And Optimization 3 · holobiomicslab

    Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational and electronic structure data as input to a machine-learning CCS prediction model.
    0 installs
18. ▌
    Chromatographic Peak Detection With Prominence Control 3 · holobiomicslab

    Use when after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature extraction in LC-MS or GC-MS metabolomics workflows.
    0 installs
19. ▌
    Consensus Spectrum Assembly From Fragmentation Spectra 2 · holobiomicslab

    Use when you have detected a single chromatographic peak in DDA LC-MS/MS data that generated multiple MS2 fragmentation spectra (e.
    0 installs
20. ▌
    Ensemble Model Weight Learning For Spectral Prediction 2 · holobiomicslab

    Use when you have pre-trained MLP and GNN models that generate different spectral predictions for the same metabolite candidates, and you want to combine them to improve ranking performance (average rank, Rank@K metrics) without retraining the base models.
    0 installs
21. ▌
    Peak Quality Assessment By Selectivity And Snr Metrics 3 · holobiomicslab

    Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence thresholds, and before mapping detected features back to individual samples or performing pre-annotation.
    0 installs
22. ▌
    Word2vec Vocabulary Matching And Unknown Peak Handling 3 · holobiomicslab

    Use when converting MS/MS spectra into Spec2Vec embeddings using a pre-trained Word2Vec model that was trained on reference data (e.g., a subset of GNPS or MassBank).
    0 installs
23. ▌
    Metabolite Feature Grouping By Adduct Isotope 2 · holobiomicslab

    Use when immediately after generating a feature table (m/z, retention time, intensity) from centroided mzML data when you need to collapse multiple feature detections of the same compound (arising from different ionization states, charge states, or isotope patterns) into unified empirical compound.
    0 installs
24. ▌
    Machine Learning Model Application To Lipidomics 2 · holobiomicslab

    Use when you have MS-DIAL lipid identifications from an Orbitrap or TOF mass spectrometer and need to remove spurious or low-confidence assignments before downstream metabolomics analysis.
    0 installs
25. ▌
    Quantum Chemistry Based Fragmentation Prediction 3 · holobiomicslab

    Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z values and intensities) to compare against experimental LC-IM-MS/MS data before performing CCS prediction or downstream.
    0 installs
26. ▌
    Ms2 Spectrum Collection From Data Dependent Acquisition 2 · holobiomicslab

    Use when you have DDA LC-MS/MS raw data (mzML format) with detected chromatographic peaks at a target m/z value and retention time window, and you need to build a high-confidence MS2 consensus spectrum for that peak to match against reference spectra (e.g., Metlin, GNPS).
    0 installs
27. ▌
    Lipid Fingerprint Regeneration Neural Networks 2 · holobiomicslab

    Use when you have MS/MS spectra with initial lipid annotations from spectral library matching (e.g., from XCMS + CAMERA or LipidIN's Expeditious Querying module) and seek to improve recall, precision, and annotation coverage.
    0 installs
28. ▌
    Ion Mobility Mass Spectrometry Data Preprocessing 3 · holobiomicslab

    Use when when you have raw IM-MS data from drift tube (DT) or SLIM instruments in Agilent MassHunter (.
    0 installs
29. ▌
    Mass Spectrometry Imaging Line Scan Data Handling 2 · holobiomicslab

    Use when you have raw line-scan MSI data from a vendor instrument (Agilent, Bruker, Thermo, or open-source .mzML format) and need to extract ion images for specified m/z targets with spatial binning and tolerance-based filtering.
    0 installs
30. ▌
    Reference Based Vs Global Coordinate Registration 2 · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples (each with mz, drift_time, retention_time, and intensity columns) and need to match corresponding features across datasets to enable cross-sample quantitation or cohort analysis.
    0 installs
31. ▌
    Blank Sample Background Interference Estimation 2 · holobiomicslab

    Use when after MS1 feature detection and accurate mass annotation, when you have identified a set of blank injections (negative controls) run in the same analytical sequence segment as your biological or study samples.
    0 installs
32. ▌
    Mass Track Construction From Centroided Spectra 3 · holobiomicslab

    Use when when you have centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment. Apply this skill at the start of an untargeted metabolomics workflow, before building a cross-sample MassGrid.
    0 installs
33. ▌
    Metabolite Feature Clustering By Retention Time 2 · holobiomicslab

    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 with retention times and intensity profiles across multiple samples and need to collapse redundant features into.
    0 installs
34. ▌
    Microbiome Metabolome Data Preprocessing 2 · holobiomicslab

    Use when when starting with raw paired microbiome (16S rRNA, metagenomic taxonomic or functional features) and metabolome (LC-MS/MS, NMR) count tables from the same biospecimens, and planning to train prediction models or co-abundance networks.
    0 installs
35. ▌
    Retention Index Assignment And Filtering 2 · holobiomicslab

    Use when after combining multiple EI or MS2 mass spectral libraries and you have access to NIST RI reference files (ri.dat and USER.DBU) and need to assign experimental retention indices to compounds.
    0 installs
36. ▌
    Spectral Library Metadata Reorganization 2 · holobiomicslab

    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 common in MoNA GC-MS and LC-MS/MS exports.
    0 installs
37. ▌
    Adduct Ion Prediction And Filtering 3 · holobiomicslab

    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 species. For example: negative-mode LC-MS or MS imaging will preferentially generate M-H and halide adducts (M+Cl);
    0 installs
38. ▌
    High Dimensional Signal Enhancement 2 · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry imaging (MSI) data with limited spatial resolution, high noise, or incomplete molecular coverage, and you want to enhance signal fidelity to support multiscale tissue–single-cell mapping or brain biochemical profiling.
    0 installs
39. ▌
    Mass Spectrum Database Matching 3 · holobiomicslab

    Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your sample.
    0 installs
40. ▌
    Nmr Metabolomic Quality Control Reporting 3 · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of plasma or serum samples, and you need to assess how processing delays affect metabolite concentrations and.
    0 installs
41. ▌
    Attention Mechanism Implementation 3 · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) datasets with peak intensity features organized as spatial graphs (nodes = pixels/voxels, edges = spatial adjacency), and you need to discover latent peak patterns for automatic peak picking or marker ion identification without manual feature.
    0 installs
42. ▌
    Autoencoder Encoder Decoder Design 3 · holobiomicslab

    Use when when working with imaging mass spectrometry (IMS) datasets where you need to extract latent low-dimensional peak features from high-dimensional peak intensity data while preserving spatial adjacency information.
    0 installs
43. ▌
    Ccs Calibration Polynomial Fitting 2 · holobiomicslab

    Use when you have acquired tunemix or reference standard data in ion mobility spectrometry with known m/z, drift time, and CCS values, and you need to establish a drift-time-to-CCS mapping for a specific instrument, ionization mode (positive or negative), and buffer gas.
    0 installs
44. ▌
    In Silico Fragmentation Prediction 2 · holobiomicslab

    Use when you have candidate metabolite structures (from database lookup or enumeration) and experimental MS/MS spectra (mzML, mzXML format), and need to rank candidates by how well their predicted fragments match observed peaks.
    0 installs
45. ▌
    Ion Mobility Heatmap Visualization 2 · holobiomicslab

    Use when you have raw LC-IMS-MS data (Agilent, Thermo, Bruker, or mzML format) and need to visualize and export the spatial distribution of a specific ion species (or ion family) across both ion mobility and retention time dimensions.
    0 installs
46. ▌
    Mass Spectrometry Metadata Caching 2 · holobiomicslab

    Use when you plan to perform repeated queries or filtering on MS metadata attributes (e.g., extract all MS2 spectra with collision energy > 30 eV, or collect all scans in a retention time window) across a large MZA HDF5 file.
    0 installs
47. ▌
    Ms1 Feature Ranking And Extraction 3 · holobiomicslab

    Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the gradient provided good separation across the chemical space.
    0 installs
48. ▌
    Proprietary Data Structure Mapping 2 · holobiomicslab

    Use when you have received raw mass spectrometry data in one of four proprietary vendor formats (Agilent '.d', Bruker ion mobility 'd', Thermo '.raw', or mzML) and need to convert it to a cross-platform, cross-language accessible format.
    0 installs
49. ▌
    Chemical Structure Fingerprint Comparison 2 · holobiomicslab

    Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method actually reflects true chemical structural similarity.
    0 installs
50. ▌
    Fragment Ion Theoretical Mass Calculation 2 · holobiomicslab

    Use when when building a comprehensive lipid fragment ion library covering all chain composition and positional isomer variants (e.g., 168.6 million entries).
    0 installs
51. ▌
    Mass Spectrometry M Z Accuracy Assessment 2 · holobiomicslab

    Use when when you have detected peaks in a direct injection FTICR-MS mzML file (or similar high-resolution MS format) and need to assess whether m/z measurements are accurate and consistent across the m/z range.
    1 install
52. ▌
    Metabolomics Peak Detection Configuration 2 · holobiomicslab

    Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram alignment.
    0 installs
53. ▌
    Microbiome Metabolome Prediction Modeling 2 · holobiomicslab

    Use when you have paired microbiome (16S rRNA, metagenomic) and metabolomic (LC-MS, GC-MS) abundance tables from the same biosamples, and you want to predict which metabolites are recoverable from microbial composition alone and identify groups of microbes and metabolites with correlated.
    0 installs
54. ▌
    Molecular Network Clustering And Analysis 3 · holobiomicslab

    Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative molecular families.
    0 installs
55. ▌
    Software Feature Inventory And Comparison 2 · holobiomicslab

    Use when you need to assess whether a newly developed FT-ICR MS pipeline (e.
    0 installs
56. ▌
    Structural Similarity Scoring Metabolites 2 · holobiomicslab

    Use when when you have paired MS/MS spectra from unknown metabolites and a reference database of known metabolites, and you want to rank candidate structures for unknown compounds by their predicted structural similarity rather than exact spectral matching.
    0 installs
57. ▌
    Chemical Database Query And Matching 3 · holobiomicslab

    Use when when you have mass-to-charge (m/z) values from mass spectrometry imaging or other MS experiments and need to assign molecular formulae with high precision, especially in spatially-resolved metabolomics where traditional LC-MS annotation methods are insufficient.
    0 installs
58. ▌
    Retention Time Window Clustering 2 · holobiomicslab

    Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you need to link individual m/z features into structural clusters representing the same metabolite in different ionization states or isotopic forms.
    0 installs
59. ▌
    Compound Identification Ranking Evaluation 3 · holobiomicslab

    Use when after training a FlavorFormer model end-to-end with weighted loss on 1H NMR spectra and compound labels, apply this skill to a held-out test set to measure compound identification accuracy and ranking quality.
    0 installs
60. ▌
    Linear Score Calculation From Coefficients 2 · holobiomicslab

    Use when when you have 1H-NMR metabolite measurements from Nightingale Health assayed on a new cohort and wish to compute risk scores (e.g., all-cause mortality, cardiovascular event, type 2 diabetes) using published metabolic biomarker weights from a reference study.
    0 installs
61. ▌
    Published Metabolic Profile Implementation 2 · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics measurements for a new cohort and wish to compute one or more established metabolic risk scores (mortality, MetaboAge, cardiovascular event, type-2 diabetes, COVID-19 severity) without recalibration.
    0 installs
62. ▌
    Biomolecular Class Label Assignment 2 · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or databases).
    0 installs
63. ▌
    Charge State Specific Peak Matching 2 · holobiomicslab

    Use when you have peak-picked features with m/z, drift_time, retention_time, and intensity columns, and you need to identify monoisotopic peaks and their charge-state-specific isotopologue members (e.g., singly charged C13-substituted species).
    0 installs
64. ▌
    Collision Cross Section Calibration 2 · holobiomicslab

    Use when you have LC-IMS-MS/MS data with drift_time measurements and need to convert raw drift times into calibrated CCS values for structural annotation.
    0 installs
65. ▌
    Collision Cross Section Computation 3 · holobiomicslab

    Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
    0 installs
66. ▌
    Comparative Omics Report Generation 2 · holobiomicslab

    Use when when you have feature lists (in CSV format) from two or more different MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), different processing software (e.
    0 installs
67. ▌
    Feature Table Consensus Aggregation 2 · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples and need to establish a unified feature catalog in which each row represents a distinct molecular entity observed across one or more samples, with harmonized m/z, drift time, and retention time coordinates.
    0 installs
68. ▌
    Format Conversion Conditional Logic 3 · holobiomicslab

    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 spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow.
    0 installs
69. ▌
    Hdf5 Output Validation Verification 2 · holobiomicslab

    Use when after invoking the DEIMoS CLI with a configuration file and allowing the Snakemake workflow to execute, use this skill to confirm successful completion of all workflow rules.
    0 installs
70. ▌
    Interference Profile Identification 3 · holobiomicslab

    Use when after running saturation repair or multidimensional smoothing on IM-MS data when you need to validate whether corrected peaks are reliable or whether overlapping coeluting/comobiling ions may have caused incorrect signal reconstruction.
    0 installs
71. ▌
    Ion Mobility Calibration Validation 2 · holobiomicslab

    Use when when you have positive- or negative-mode ion mobility spectrometry data with tunemix reference standards (known m/z, drift times, and CCS values) and need to verify that the calibration model accurately captures the relationship between drift time, reference m/z, and collision cross.
    0 installs
72. ▌
    Metabolite Taxonomy Database Lookup 2 · holobiomicslab

    Use when when you have MS/MS-annotated features from a natural extract (via SIRIUS, CANOPUS, or ISDB) and need to compute the Literature Component or Class Component of a priority rank—i.
    2 installs
73. ▌
    Multidimensional Feature Annotation 2 · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic signatures to distinguish monoisotopic peaks from isotopologues, reduce feature redundancy, and support multi-dimensional.
    0 installs
74. ▌
    Multidimensional Ms Data Conversion 2 · holobiomicslab

    Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments, and you need to: (1) store multidimensional spectra in a vendor-neutral, platform-agnostic format;
    0 installs
75. ▌
    Singly Charged Ion Mass Calculation 2 · holobiomicslab

    Use when you have detected monoisotopic features (m/z, drift_time, retention_time, intensity) from LC-IMS-MS/MS data and need to identify and cluster their C13 isotopologues for charge state z=+1.
    0 installs
76. ▌
    Spectral Peak Binning Preprocessing 2 · holobiomicslab

    Use when when you have raw high-resolution tandem mass spectra (mzML, mzXML, or MGF format) that you intend to cluster or compare at scale, and you need to convert continuous m/z and intensity measurements into discrete bins suitable for feature hashing or similarity searching.
    0 installs
77. ▌
    Transition Group Feature Extraction 2 · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA mass spectrometry data) and need to identify precise peak boundaries, apex retention/drift time, and intensity values for quantitative feature detection.
    0 installs
78. ▌
    Gc Ms Data Preprocessing And Normalization 3 · holobiomicslab

    Use when you have raw GC-MS data (aroma, breath, or other volatile analyte samples) in NetCDF or vendor-native format and need to identify multivariate chemo-/biomarker features without conventional peak picking.
    0 installs
79. ▌
    Left Censored Missing Value Classification 3 · holobiomicslab

    Use when you have a metabolomics dataset (LC/MS or GC/MS) with missing values and need to determine which are below the limit of detection (LOD) or limit of quantification (LOQ). Left-censored classification is necessary when the missingness is informative—i.
    0 installs
80. ▌
    Metabolic Age Prediction From Nmr Features 2 · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics data (feature matrix with named metabolite columns) and need to compute predicted metabolic age for each sample, typically to assess whether individuals' metabolic profiles align with or diverge from age-expected trajectories.
    0 installs
81. ▌
    Metabolomics Imputation Method Application 3 · holobiomicslab

    Use when your metabolomics dataset (LC/MS or GC/MS) contains missing values encoded as NA or zero that represent compounds below the instrument's limit of detection (LOD) or limit of quantification (LOQ), rather than values missing completely at random.
    0 installs
82. ▌
    Multi Task Attention Mechanism Integration 2 · holobiomicslab

    Use when when baseline MLP or GNN models for spectral prediction show limited performance on metabolite annotation tasks, and you have access to auxiliary spectral topic labels (e.g., via LDA on spectral features) that could provide regularization signal.
    0 installs
83. ▌
    Spectral Database Integration And Sampling 2 · holobiomicslab

    Use when you need to generate synthetic LC/GC-MS feature tables or raw mzML files with realistic peak complexity, ion multiplicities, and natural spectral variation—not just theoretical m/z values.
    0 installs
84. ▌
    Spectral Vector Normalization By Intensity 3 · holobiomicslab

    Use when when converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring. Specifically, apply this skill after you have represented individual peaks and neutral losses as words ('[redacted-email]', 'loss@xxx.
    0 installs
85. ▌
    Biological Reactant Pair Mapping Kegg 3 · holobiomicslab

    Use when constructing or enriching a chemical formula database that must capture not just structural similarity (DBEdges) but also biological co-occurrence patterns.
    0 installs
86. ▌
    Msi Data Matrix Import And Validation 2 · holobiomicslab

    Use when you have MSI intensity data exported from MSiReader, SCiLS, or Cardinal as plain-text CSV files or as Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment objects, and need to load it into R as a validated msimat object for mass difference and adduct analysis.
    0 installs
87. ▌
    Spectral Similarity Matching And Comparison 2 · holobiomicslab

    Use when after extracting and optionally combining MS2 spectra from a chromatographic peak (e.g., at a known m/z value like 304.1131), you need to determine which compound(s) in a reference library match the experimental spectrum.
    0 installs
88. ▌
    Environment Dependency Management 2 · holobiomicslab

    Use when when deploying Galaxy-M or similar multi-component metabolomics platforms that depend on heterogeneous runtime environments (Python, R, MATLAB, WINE) across multiple operating systems (Ubuntu 14.
    0 installs
89. ▌
    Ion Image Quantification Workflow 3 · holobiomicslab

    Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.
    0 installs
90. ▌
    Mass Track Extraction And Binning 3 · holobiomicslab

    Use when when you have centroid mzML files from LC-MS metabolomics acquisition and need to construct sample-level mass tracks before cross-sample alignment. Specifically: you are starting fresh with vendor-converted or pre-processed mzML input;
    0 installs
91. ▌
    Peak Detection And Mass Alignment 2 · holobiomicslab

    Use when when you have raw LC-MS/MS data files (.mzML, .raw, or vendor formats) from multiple samples and need to identify reproducible molecular features across the cohort before annotation or statistical analysis.
    0 installs
92. ▌
    Chromatogram Peak Boundary Detection 2 · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA-MS data) and need to identify precise peak boundaries and apex positions for feature extraction.
    0 installs
93. ▌
    Graph Clustering Community Detection 2 · holobiomicslab

    Use when after constructing a spectral similarity network from pairwise cosine similarity scores between deconvolved GC-MS spectra.
    0 installs
94. ▌
    Ion Mobility Dimension Interpolation 3 · holobiomicslab

    Use when when processing raw IM-MS data (Agilent MassHunter .
    0 installs
95. ▌
    Mass Spectrometry Metric Engineering 2 · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to quantify file quality for automated quality control, longitudinal instrument monitoring, or training a quality prediction classifier.
    0 installs
96. ▌
    Mass Tolerance Parameter Calibration 2 · holobiomicslab

    Use when when converting raw line-scan mass spectrometry imaging data (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .mzML formats) and must decide which m/z values from a reference mass list correspond to peaks in the raw spectra.
    0 installs
97. ▌
    Physicochemical Property Computation 2 · holobiomicslab

    Use when you have one or more peptide or protein sequences in string format and need to calculate their mass, isotopic envelope (m/z and intensity pairs), charge state behavior, isoelectric point, or predicted chromatographic retention.
    0 installs
98. ▌
    Prm Acquisition Event Identification 2 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is happening at regular intervals consistent with your instrument method design.
    0 installs
99. ▌
    Savitzky Golay Smoothing Application 2 · holobiomicslab

    Use when after filtering retention time and drift time ranges on raw GCIMS samples but before decimation and alignment.
    0 installs
100. ▌
     Simulation Control Loop Architecture 2 · holobiomicslab

     Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic window selection) would perform without access to real instrument time.
     0 installs