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HolobiomicsLab

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1. ▌
   Retention Time Feature Clustering 2 · holobiomicslab

   Use when after chromatographic peak detection (findChromPeaks) when you have a processed XcmsExperiment object with detected peaks and need to perform initial feature grouping. Use it when features of the same compound are expected to co-elute within a narrow retention-time window (e.
   0 installs
2. ▌
   Structure Prediction From Spectra 2 · holobiomicslab

   Use when you have experimental mass spectrometry spectra (LC–QTOF or similar format) from unknown compounds and need to predict their molecular structures.
   0 installs
3. ▌
   Dia File Quality Prediction 2 · holobiomicslab

   Use when you have a batch of DIA mass spectrometry raw files (.raw, .d, or .wiff formats) from known instrument types (timsTOF, TripleTOF, or Orbitrap) and need to classify each file as pass/fail or assign a quality label.
   0 installs
4. ▌
   Instrument Metadata Parsing 2 · holobiomicslab

   Use when when you have raw or semi-processed mass spectrometry data files in mixed formats (e.g., vendor-native .raw, .d, .
   0 installs
5. ▌
   Java Source Code Inspection 2 · holobiomicslab

   Use when when you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format types (e.
   0 installs
6. ▌
   Mnar Data Handling 3 · holobiomicslab

   Use when you have metabolomics data (targeted LC/MS or untargeted GC/MS) with left-censored missing values below the limit of quantification (LOQ) or limit of detection (LOD), and you need to impute these values while preserving the underlying distributional structure and avoiding bias from.
   0 installs
7. ▌
   2d Tic Preprocessing 2 · holobiomicslab

   Use when when you have raw GCxGC-MS data imported from NetCDF into a 2D-TIC chromatogram object and need to remove chemical and instrumental noise (column bleeding, baseline drift, detector contamination) to reveal metabolite differences between sample groups for downstream multiway PCA or.
   0 installs
8. ▌
   Ms Data Preprocessing 2 · holobiomicslab

   Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted metabolomics workflow (e.g., AriumMS) that requires standardized, interoperable file formats.
   0 installs
9. ▌
   Mzml File Import Xcms 2 · holobiomicslab

   Use when you have raw mzML files from a mass spectrometry instrument and need to begin a preprocessing workflow in xcms. This is the essential first step before any peak detection (centWave, MSWParam) or feature grouping can occur.
   0 installs
10. ▌
    Mass Spectrum M Z Alignment 2 · holobiomicslab

    Use when when working with multidimensional MS data (LC–IM–MS/MS) converted to MZA format where spectra are stored in jagged arrays with m/z values distributed across individual HDF5 datasets per scan, and you need to ensure m/z consistency for downstream peak detection, isotope analysis, or.
    0 installs
11. ▌
    Mass Spectrum Visualization 2 · holobiomicslab

    Use when when you have extracted m/z and intensity arrays from an MZA file (or similar HDF5-backed MS data structure) and need to visually inspect a single MS1 or MS2 spectrum, verify peak characteristics, or diagnose data quality issues before downstream analysis (peak fitting, isotope pattern.
    0 installs
12. ▌
    Ppm Mass Accuracy Filtering 3 · holobiomicslab

    Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes. Apply this skill after importing the .imzML metadata and .
    0 installs
13. ▌
    R Data Structure Processing 2 · holobiomicslab

    Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100 s) and drift time (5–16 ms) ranges, or when you need to apply smoothing, decimation, or baseline correction to raw GCIMS.
    0 installs
14. ▌
    Reactant Ion Peak Exclusion 2 · holobiomicslab

    Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion source) would otherwise be misidentified as an analyte peak, causing false positives in the peak list.
    0 installs
15. ▌
    Retention Time Mz Alignment 2 · holobiomicslab

    Use when processing raw LC/MS data (mzML or mzXML format) from multi-sample cohorts where retention time or intensity drift is suspected due to batch effects, instrument calibration drift, or variable run order.
    0 installs
16. ▌
    Bioassay Activity Data Integration 2 · holobiomicslab

    Use when when you have (1) a molecular network graph from GNPS with node identifiers and edges, (2) LC-MS/MS features quantified across fractions in a feature table, and (3) bioassay measurements (e.
    0 installs
17. ▌
    Chromatographic Peak Detection Msw 2 · holobiomicslab

    Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time dimensions. Use this skill when you must isolate individual ion signals before applying calibration corrections (e.
    0 installs
18. ▌
    Mass Spectrometry Feature Grouping 2 · holobiomicslab

    Use when after raw data processing and feature extraction (e.g., via XCMS, OpenMS, or enviPick) when you have detected features across multiple LC-MS or GC-MS analyses and need to identify which features represent the same chemical across samples.
    0 installs
19. ▌
    Mass Spectrometry Library Matching 3 · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (with ≥10 peaks, precursor m/z, and at least 5 fragment ions) and need to identify it by comparing against a curated spectral library with annotated InChIKeys or chemical structures.
    0 installs
20. ▌
    Metabolomics Software Benchmarking 3 · holobiomicslab

    Use when you have completed peak picking with two or more competing tools (e.g., IDSL.IPA, MZmine 2, xcms, MS-DIAL) on the same LC/HRMS dataset(s) and need to quantify which performs better. Use this skill when tool selection claims require validation (e.g., 'IDSL.
    0 installs
21. ▌
    Noise Suppression Spectral Imaging 3 · holobiomicslab

    Use when your input is a raw two-dimensional MS map (m/z vs retention time) derived from chromatography–mass spectrometry data with poor signal-to-noise characteristics, and you need to discriminate individual analytes and identify marker features reliably.
    0 installs
22. ▌
    Pathway Ranking And Prioritization 3 · holobiomicslab

    Use when after peak annotation when you have: (1) a peak intensity matrix (rows=peaks with KEGG/ChEBI/UniProt IDs, columns=samples) with group labels; (2) a pathway database (KEGG, Reactome, or user-defined metabolite sets); (3) a comparative experimental design (case vs. control groups).
    0 installs
23. ▌
    Peak Picking Avoidance Ms Analysis 3 · holobiomicslab

    Use when analyzing raw 2D MS data (m/z vs. retention time maps) where conventional peak picking introduces unacceptable error rates, particularly in untargeted metabolomics or chemometrics studies requiring sensitive marker identification at trace levels (e.g., parts per billion).
    0 installs
24. ▌
    Ms2 Annotation Interpretation 3 · holobiomicslab

    Use when after GNPS spectral library search has returned matched chemical annotations (with m/z values and cosine similarity scores) for MS/MS spectra.
    0 installs
25. ▌
    Hmdb Metabolite Query And Retrieval 2 · holobiomicslab

    Use when you have identified one or more proton NMR spectral regions-of-interest (ROIs)—defined by lower and upper chemical-shift bounds in ppm—from complex biological samples (serum, saliva, urine, tissue, CSF) and need to generate a ranked list of plausible metabolite identities.
    0 installs
26. ▌
    Ms Ms Spectrum Preprocessing 4 · holobiomicslab

    Use when you have raw or semi-processed MS/MS spectral data from bottom-up tandem mass spectrometry experiments (data-dependent acquisition) that you intend to input to de novo peptide sequencing tools like Casanovo.
    0 installs
27. ▌
    Noise Level Parameter Tuning 2 · holobiomicslab

    Use when when you have an aligned GCIMS dataset and need to configure the findPeaks function with CWT algorithm to detect peaks across retention time and drift time dimensions.
    0 installs
28. ▌
    Sterol Isomer Classification 3 · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from sterol-containing tissue samples and need to assign detected peaks to specific structural isomers (e.g., distinct double bond positions or saturation patterns in C27–C29 sterols).
    0 installs
29. ▌
    Deep Learning Metabolite Annotation 3 · holobiomicslab

    Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible format) from a water sample, a precursor m/z and retention time of interest, and want to annotate an unknown compound by predicting its molecular formula, structure, and name using deep learning scoring rather than.
    0 installs
30. ▌
    Eic Similarity Correlation Analysis 2 · holobiomicslab

    Use when after abundance-correlation-based feature group refinement when you observe that larger feature groups (particularly those with 3+ features in the same m/z–retention-time window) may contain features with different peak shapes or retention-time shifts in their EICs, or when abundance.
    0 installs
31. ▌
    Mass Spectrometry Raw Data Encoding 2 · holobiomicslab

    Use when you have generated or obtained a two-dimensional mass-spectrometry intensity matrix (m/z × retention time scan points) with simulated or experimental peak shapes, noise, and background, and need to encode it as a binary .
    0 installs
32. ▌
    Mass Spectrum Structure Elucidation 2 · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision-induced dissociation, CID) and a known chemical formula (or narrow set of candidate formulas), and you need to identify the most likely structure(s) by ranking against a large candidate library such as PubChem.
    0 installs
33. ▌
    Metabolite Library Entry Generation 2 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (from MassBank or your own acquisition) and need to create a standardized library entry with ranked fragment ions for use in MetaboAnnotatoR or other fragment-based annotation pipelines.
    0 installs
34. ▌
    Metabolomic Feature Table Filtering 2 · holobiomicslab

    Use when after feature detection (e.g., Asari processing of mzML files to feature tables) but before normalization, batch correction, or annotation.
    0 installs
35. ▌
    Metabolomics Feature Table Curation 2 · holobiomicslab

    Use when you have a raw feature table (TSV/CSV) derived from LC-MS peak detection (e.
    0 installs
36. ▌
    Metabolomics Feature Transformation 2 · holobiomicslab

    Use when when you have a feature intensity table (samples × compounds) from targeted or non-targeted metabolomics and need to prepare it for statistical modeling or multivariate analysis.
    0 installs
37. ▌
    Rank Performance Metric Computation 2 · holobiomicslab

    Use when when you have predictions from one or more metabolite annotation models (MLP baseline, GNN, or ESP ensemble) and need to quantify ranking performance on ESI/LC-MS test spectra.
    0 installs
38. ▌
    Two Dimensional Ms Image Processing 3 · holobiomicslab

    Use when you have raw GC–MS or LC–MS data represented as a two-dimensional map (m/z axis vs. retention time axis) and need to identify chemo-/biomarker features across multiple analytes simultaneously, especially when conventional peak picking produces high false-positive or false-negative rates.
    0 installs
39. ▌
    Whittaker Smoother Signal Denoising 2 · holobiomicslab

    Use when after baseline correction (e.g., via asymmetric least squares) when raw GCxGC-MS chromatograms still contain high-frequency noise that obscures true signal structure. Use it when you need to reduce noise before peak alignment or multivariate analysis (e.
    0 installs
40. ▌
    Feature Statistical Annotation 2 · holobiomicslab

    Use when after LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes. Use this skill when you have access to a reference list of molecules of interest (e.
    0 installs
41. ▌
    Metabolite Annotation At Scale 3 · holobiomicslab

    Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign putative metabolite identities using public structural databases.
    0 installs
42. ▌
    Spatial Coordinate Mapping Msi 3 · holobiomicslab

    Use when after loading and preprocessing a Cardinal MSImagingExperiment object (with normalized peaks and optional spatial segmentation results), and before conducting spatial statistical tests or co-localization analyses.
    0 installs
43. ▌
    Transformer Model Training 2 · holobiomicslab

    Use when you have a dataset of augmented simulated overlapped GC-MS peaks and need to train a Transformer model to automatically deconvolve them into pure component mass spectra.
    1 install
44. ▌
    Conditional Routing Logic Extraction 2 · holobiomicslab

    Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing pipelines.
    0 installs
45. ▌
    Cross Assay Feature Linkage Analysis 2 · holobiomicslab

    Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.
    0 installs
46. ▌
    Xcms Feature Extraction And Grouping 2 · holobiomicslab

    Use when you have raw mzXML LC/MS files from replicated metabolomics experiments (e.g., 12 samples across labeled/unlabeled conditions) and need to extract, align, and group peaks before downstream feature filtering (e.g., fold-change or isotope enrichment analysis).
    0 installs
47. ▌
    Cross Sample Feature Matching 2 · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples and need to establish correspondence between features across samples to enable quantitative comparison, statistical analysis, or consensus feature calling.
    0 installs
48. ▌
    Fixed Size Integration Method 2 · holobiomicslab

    Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.
    0 installs
49. ▌
    Gcims Dataset Object Creation 2 · holobiomicslab

    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 preprocessing pipeline.
    0 installs
50. ▌
    Hdf5 Hierarchical Data Access 2 · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format (from Agilent .d, Bruker .d with ion mobility, Thermo .
    0 installs
51. ▌
    Latent Feature Interpretation 3 · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) data preprocessed into an h5py-backed feature matrix, and a trained graph-attention autoencoder has already extracted latent low-dimensional peak features.
    0 installs
52. ▌
    M Z Tolerance Window Matching 2 · holobiomicslab

    Use when when you have detected features with m/z, drift time, and retention time dimensions and need to associate peaks into isotopic groups (e.g., monoisotopes with C13 substitutions) or align features across multiple LC-IMS-MS/MS samples.
    0 installs
53. ▌
    Ms Data Format Identification 2 · holobiomicslab

    Use when when receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline. Specifically, apply this skill when: (1) input files arrive without documented instrument type or chromatographic/mobility dimensionality;
    0 installs
54. ▌
    Quantitation Table Generation 2 · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a defined list of m/z, retention time, or other identifiers for which you need to extract and quantify peak abundances across one or more samples.
    0 installs
55. ▌
    Signal Residual Deconvolution 2 · holobiomicslab

    Use when analyzing 1D signal arrays (e.g., extracted ion chromatograms, arrival time distributions, or MS1 spectra intensity profiles) where multiple peaks may overlap or where peak shape information (amplitude, position, width) is required beyond simple local-maximum detection.
    0 installs
56. ▌
    Compound Identification From Ms Data 2 · holobiomicslab

    Use when you have raw GC-MS or LC-MS data in vendor format (NetCDF, .raw, .d) or generic mass lists, and you need to assign chemical identities to detected peaks.
    0 installs
57. ▌
    Compound Isotope And Adduct Grouping 2 · holobiomicslab

    Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per compound. Use it when your data contains isotopic peaks (e.g., ¹³C variants) and multiple ionization products (e.
    0 installs
58. ▌
    Feature Pair Scoring In Metabolomics 2 · holobiomicslab

    Use when use this skill after XCMS feature detection and alignment on non-targeted LC-MS or GC-MS metabolomics data, when you have aligned features with quantitative profiles across samples and need to group features that co-originate from the same compound (accounting for isotopic peaks, adducts.
    0 installs
59. ▌
    Gc Ms Spectral Similarity Clustering 2 · holobiomicslab

    Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct a molecular network.
    0 installs
60. ▌
    Left Censored Missingness Simulation 3 · holobiomicslab

    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 evaluating imputation algorithm performance.
    0 installs
61. ▌
    Metabolomic Feature Table Processing 2 · holobiomicslab

    Use when you have a metabolomics feature table (rows=features, columns=samples) generated from LC-MS or GC-MS preprocessing and need to identify which features contain systematic errors from peak integration or alignment.
    0 installs
62. ▌
    Missing Data Mechanism Specification 3 · holobiomicslab

    Use when when you have a metabolomics abundance table with missing values and need to decide which imputation method to apply, or when designing a simulation to evaluate imputation performance.
    0 installs
63. ▌
    Nmr Chemical Shift Interval Matching 2 · holobiomicslab

    Use when you have isolated one or more regions-of-interest (ROIs) from a proton NMR spectrum (defined as lower and upper chemical-shift bounds in ppm) and need to systematically generate a list of plausible metabolite assignments from a reference database.
    0 installs
64. ▌
    Peak Picking Parameter Configuration 2 · holobiomicslab

    Use when when reconstructing a metabolite fragment library entry from raw MS/MS spectral data (e.g., from MassBank or local acquisition), you need to define peak-picking thresholds to separate true fragment ions from baseline noise and assign occurrence scores.
    0 installs
65. ▌
    Spectral Library Metadata Assignment 2 · holobiomicslab

    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 capillary GC-MS workflows.
    0 installs
66. ▌
    Spectrum Peak Counting And Reporting 2 · holobiomicslab

    Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a selected noise-filtering strategy retains an expected number of peaks for downstream molecular formula assignment.
    0 installs
67. ▌
    Unannotated Feature Characterization 2 · holobiomicslab

    Use when you have aligned feature tables from LC–MS/MS, corresponding in silico annotations (from GNPS/ISDB or SIRIUS), and metadata describing sample origin. Use it to rank extracts by the proportion of sample-specific, unannotated features—a proxy for structural novelty.
    0 installs
68. ▌
    Spectral Data Normalization Tic 3 · holobiomicslab

    Use when apply TIC normalization when you have raw, unprocessed mass spectrometry data (Cardinal objects or imaging matrices with 10,000+ m/z features and 1,000+ spectra) where signal intensity varies across spatial locations or samples due to instrumental drift, uneven sample preparation, or.
    0 installs
69. ▌
    4d Lcimmsms Feature Extraction 3 · holobiomicslab

    Use when you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values against a quantum chemistry calculation-assisted CCS prediction database.
    0 installs
70. ▌
    Chromatography Data Decimation 2 · holobiomicslab

    Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g., 5–16 ms) ranges and applying Savitzky-Golay smoothing. Use it as a preprocessing step before alignment operations.
    0 installs
71. ▌
    Cluster Statistics Integration 2 · holobiomicslab

    Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did not yield detected peaks at certain cluster positions.
    0 installs
72. ▌
    Control Flow Diagram Synthesis 2 · holobiomicslab

    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 declared input type (LC, GC, IMS, or MS Imaging).
    0 installs
73. ▌
    Drift Retention Time Alignment 2 · holobiomicslab

    Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature fluctuations or chromatographic column degradation, and you need to normalize sample positions before downstream peak.
    0 installs
74. ▌
    Gc Ims Matrix Table Generation 2 · holobiomicslab

    Use when after integratePeaks has been executed with a chosen integration method (e.g., fixed_size with RIP saturation threshold of 0.1) on a clustered, baseline-corrected GC-IMS dataset.
    0 installs
75. ▌
    Multi Panel Spectra Comparison 2 · holobiomicslab

    Use when when you need to visually compare two or more spectra (MS1, MS2, or extracted ion chromatograms) across different retention times, m/z ranges, or ion mobility bins in a single figure. Apply this skill after extracting spectra arrays from MZA files (e.
    0 installs
76. ▌
    Thermo Raw File Format Parsing 2 · holobiomicslab

    Use when you have acquired multidimensional mass spectrometry data (MS1, MS/MS, or data-independent acquisition) from a Thermo instrument saved in the proprietary '.
    0 installs
77. ▌
    Workflow Routing Configuration 2 · holobiomicslab

    Use when when you have raw mass spectrometry data files from multiple acquisition modalities (LC-MS, GC-MS, ion mobility, or imaging) and need to automatically route each to the correct downstream analysis module without manual intervention.
    0 installs
78. ▌
    Corpus Size Coverage Scaling Analysis 3 · holobiomicslab

    Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's learned peak embeddings sufficiently represent the peaks in your query spectra.
    0 installs
79. ▌
    Cosine Similarity Spectral Clustering 2 · holobiomicslab

    Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural relationships and enable compound annotation.
    0 installs
80. ▌
    Mass Spectrum Fragment Ion Extraction 2 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or acquired data) for a single metabolite with known accurate precursor m/z and adduct type, and you need to generate a library entry with scored fragments for use in metabolite annotation pipelines.
    0 installs
81. ▌
    Metabolite Tandem Ms Library Curation 2 · holobiomicslab

    Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural annotations (missing SMILES or molecular formula fields) and need to combine them into unified, polarity-specific msp files.
    0 installs
82. ▌
    Neutral Loss Extraction And Weighting 3 · holobiomicslab

    Use when you have a collection of annotated MS/MS spectra with precursor m/z values and fragment peak lists, and you aim to train or apply a spectral similarity model (such as Spec2Vec Word2Vec) that exploits fragmentation chemistry.
    0 installs
83. ▌
    Noise Artifact Reduction Optimization 2 · holobiomicslab

    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 obscure true metabolite signals and impede between-group differentiation in downstream multivariate analysis.
    0 installs
84. ▌
    Retention Time Based Feature Grouping 2 · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data when you have an xcms result object (XcmsExperiment or xcmsSet) with detected peaks and need to collapse redundant m/z signals into feature groups.
    0 installs
85. ▌
    Spectral Library Molecular Networking 2 · holobiomicslab

    Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their similarity relationships, and identify spectral families without prior library matching.
    0 installs
86. ▌
    Temporal Profile Correlation Analysis 2 · holobiomicslab

    Use when you have time-resolved direct injection mass spectrometry data (e.
    0 installs
87. ▌
    Two Dimensional Spectral Map Analysis 3 · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map with m/z values on one axis and retention time on the other, and you need to identify analyte signals and chemo-/biomarker features while minimizing false positive and false negative peak detections.
    0 installs
88. ▌
    Mass Spectral Feature Annotation 3 · holobiomicslab

    Use when you have m/z values from spatially-resolved mass spectrometry imaging (e.g., MALDI-MSI, DESI-MSI) and need to assign molecular formulae to thousands of features with higher precision than traditional LC-MS approaches.
    0 installs
89. ▌
    Spatial Overlap Analysis Imaging 2 · holobiomicslab

    Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit overlapping spatial distributions across the tissue image that could confound downstream annotation filtering.
    0 installs
90. ▌
    Fragment Ion Peak Annotation 2 · holobiomicslab

    Use when you have experimental MS/MS spectra matched against a reference library (via cosine similarity or dot-product scoring) and need to map individual fragment peaks in the experimental spectrum to their corresponding m/z and intensity values in the matched library entry.
    0 installs
91. ▌
    Knime Workflow Orchestration 2 · holobiomicslab

    Use when you have raw LC-MS data (mzML, NetCDF) from multiple runs that require sequential feature detection, alignment, quantification, and optional filtering (e.g., blank exclusion, QC reproducibility, retention-time outlier removal) before spatial mapping or annotation.
    0 installs
92. ▌
    Metabolomics Tool Deployment 2 · holobiomicslab

    Use when you have a Galaxy installation (specifically Galaxy Master branch commit c429777c93680dcee449fe410f5360afbe673758 or compatible) and need to add metabolomics analysis capabilities including tools for XCMS integration, mass spectrometry file reading (via MSFileReader), and metabolite.
    0 installs
93. ▌
    Targeted Peak Extraction Ms1 2 · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify.
    0 installs
94. ▌
    Binary Spectral Data Extraction 3 · holobiomicslab

    Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
    0 installs
95. ▌
    Cross Software Feature Matching 2 · holobiomicslab

    Use when you have collected feature lists in CSV format from two or more MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), processing software packages (e.g., vendor-specific vs. open-source), or instrument platforms (e.
    0 installs
96. ▌
    Isotope Mass Offset Enumeration 2 · holobiomicslab

    Use when you have a detected feature table (m/z, drift_time, retention_time, intensity) from LC-IMS-MS or similar multidimensional MS data and want to identify and annotate isotopic families (e.g., singly-charged C13 patterns).
    0 installs
97. ▌
    Machine Learning Model Training 2 · holobiomicslab

    Use when you have a labeled dataset of DIA raw files (.raw, .d, .wiff) with known quality annotations and have extracted the 15 iDIA-QC metrics (raw file characteristics from timsTOF, TripleTOF, or Orbitrap instruments).
    0 installs
98. ▌
    Peak Detection Cwt Optimization 2 · holobiomicslab

    Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.
    0 installs
99. ▌
    Spectral Peak Clustering Gc Ims 2 · holobiomicslab

    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 comparison and quantification.
    0 installs
100. ▌
     Chromatographic Peak Detection Wavelet 2 · holobiomicslab

     Use when you have loaded raw LC-MS or direct-injection FTICR-MS data (in mzML or netCDF format) into an XCMSnExp object and need to identify individual chromatographic peaks before feature grouping.
     0 installs