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HolobiomicsLab

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1. ▌
   Annotation Table Construction 2 · holobiomicslab

   Use when when you have access to multiple public metabolomics databases and need to build a unified reference table for metabolite annotation in untargeted mass spectrometry analysis.
   0 installs
2. ▌
   Biotransformation Enumeration 2 · holobiomicslab

   Use when you have a known parent drug chemical formula and aim to predict its metabolite landscape prior to or during high-resolution mass spectrometry analysis (mzML).
   0 installs
3. ▌
   Chemical Formula Manipulation 2 · holobiomicslab

   Use when when you have a parent drug's raw chemical formula and need to predict its potential metabolites in mass spectrometry data (mzML format) to match against observed peaks.
   0 installs
4. ▌
   Deep Learning Model Inference 3 · holobiomicslab

   Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to classify unknown compounds or generate prediction confidence scores for structural novelty analysis.
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5. ▌
   Embedding Similarity Matching 2 · holobiomicslab

   Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, and you need to identify the most likely candidate molecules from a reference database.
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6. ▌
   Joint Embedding Space Scoring 2 · holobiomicslab

   Use when you have a mass spectrum from an untargeted metabolomics experiment and a set of candidate molecules (e.g., downloaded from PubChem) that may explain that spectrum. You want to rank these candidates by likelihood of correctness to prioritize manual annotation or further validation.
   0 installs
7. ▌
   Least Squares Optimization 1d 2 · holobiomicslab

   Use when when you have a 1D signal array (e.g., extracted ion chromatogram, arrival time distribution, or MS1 spectrum intensity profile) and need to identify and quantify overlapping or adjacent peaks with precise position, height, and width estimates.
   0 installs
8. ▌
   Query Language Grammar Design 2 · holobiomicslab

   Use when when you need to enable non-programmer mass spectrometry users to express complex spectral search patterns (e.g., isotope patterns, precursor mass constraints, scan-type filters) without writing procedural code.
   0 installs
9. ▌
   Random Walk Graph Propagation 2 · holobiomicslab

   Use when you have: (1) a set of spectral library matches (seed identities) mapped to molecular structures, (2) a candidate structure graph derived from in silico fragmentation (e.
   0 installs
10. ▌
    Smiles Parsing And Validation 3 · holobiomicslab

    Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing descriptors, generating mass spectra, or calculating chemical fingerprints.
    0 installs
11. ▌
    Spectral Peak Feature Hashing 2 · holobiomicslab

    Use when when you have a large collection of query high-resolution mass spectra that must be rapidly matched against a spectral library containing modified and unmodified peptides, and you need to reduce computational overhead before approximate nearest neighbor indexing or GPU-accelerated.
    0 installs
12. ▌
    Spectrum Object Instantiation 2 · holobiomicslab

    Use when after successfully parsing raw spectral data from one of the supported file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) into intermediate dictionaries containing m/z arrays, intensity arrays, and metadata key-value pairs.
    0 installs
13. ▌
    Spectrum Object Schema Design 2 · holobiomicslab

    Use when when building a mass spectrometry data import pipeline that must ingest spectra from multiple file formats and produce a unified, queryable representation suitable for metadata validation, peak filtering, and similarity comparisons.
    0 installs
14. ▌
    Ion Image Augmentation Design 3 · holobiomicslab

    Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that reflect either co-localization relationships between different molecular ions (COL mode) or isotopic relationships.
    0 installs
15. ▌
    Chemical Identifier Verification 2 · holobiomicslab

    Use when when you have a list of chemically known compounds and need to validate that an MS processing pipeline (e.g., mzExacto) correctly retrieves their characteristic m/z, retention time, match factor, and area values from GC-MS data.
    0 installs
16. ▌
    Chemical Phylogenetic Comparison 2 · holobiomicslab

    Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1 features to each other based on predicted molecular substructures and chemical properties rather than arbitrary.
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17. ▌
    Conditional Logic Implementation 2 · holobiomicslab

    Use when you have a user-submitted spectrum with domain-context metadata (e.
    0 installs
18. ▌
    Feature Annotation Consolidation 2 · holobiomicslab

    Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to consolidate redundant or related ion signals into compound-level feature groups before downstream statistical or.
    0 installs
19. ▌
    Feature Table Moniker Management 2 · holobiomicslab

    Use when when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to track which version of the table is being used at each step.
    0 installs
20. ▌
    Ion Count Percentage Calculation 2 · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to an mpactr object and generating a qc_summary() data.
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21. ▌
    Ion Type Assignment Verification 2 · holobiomicslab

    Use when after calling MsmsSpectrum.annotate_proforma() to assign fragment ions to a mass spectrum, verify that each annotated peak has the correct ion_type ('b' or 'y'), charge state, and m/z deviation from the theoretical mass computed for that peptidoform.
    0 installs
22. ▌
    Isotopologue Signature Detection 2 · holobiomicslab

    Use when you have preprocessed, statistically significant LC-MS features (from multiple assays or a single assay) and need to group features that represent the same metabolite in different isotopic labeling states.
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23. ▌
    JSON Parsing Motifset Extraction 2 · holobiomicslab

    Use when you have completed the MS2LDA LDA modeling phase and possess motifset.json or motifset_optimized.json files containing inferred Mass2Motifs.
    0 installs
24. ▌
    Lantibiotic Structure Annotation 2 · holobiomicslab

    Use when you have (1) genomic data from a Streptomyces or other RiPP-producing organism in raw FASTA format or annotated GenBank format, (2) high-resolution LC-MS/MS spectra in centroided MGF, mzML, mzXML, or mzData format, and (3) a known or predicted lantibiotic core peptide sequence you wish to.
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25. ▌
    Lc Ms Quality Metric Computation 2 · holobiomicslab

    Use when after performing peak detection on centroided .mzML LC-MS data with screening_mode=FALSE in TARDIS.
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26. ▌
    Lcms Target Visibility Screening 2 · holobiomicslab

    Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.
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27. ▌
    Lipid Library Annotation From Mz 2 · holobiomicslab

    Use when you have experimental peaklist data (CSV or mzML-derived tables) from UHPLC-HRMS/MS instruments (Q-Exactive, Agilent/Bruker/SCIEX Q-TOF) with fragment m/z values and want to annotate them to known lipid identities.
    0 installs
28. ▌
    Mass Difference Pattern Matching 2 · holobiomicslab

    Use when after peak picking and sample alignment when you have an aligned feature table containing m/z and retention time coordinates. Use it when your untargeted LC-MS workflow needs to reduce feature redundancy caused by naturally occurring stable isotope patterns and common adduct formation.
    0 installs
29. ▌
    Metabolite Spectral Data Merging 2 · holobiomicslab

    Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of in-house standards in separate MSP files) and need to combine them with consistent metadata (SMILES, InChIKey, molecular.
    0 installs
30. ▌
    Ms2 Diagnostic Fragment Matching 2 · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent LC- or GC-HRMS measurements and need to rapidly prioritize potential PFAS features within a larger feature set.
    0 installs
31. ▌
    Neutral Loss Peak Interpretation 2 · holobiomicslab

    Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.
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32. ▌
    Pfas Homologous Series Detection 2 · holobiomicslab

    Use when you have an m/z-resolved feature list from LC- or GC-HRMS analysis (either detected by pyOpenMS or provided as a custom Excel table) and need to prioritize potential PFAS compounds by identifying clusters of homologous structures.
    0 installs
33. ▌
    Raw File Data Extraction Via API 2 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.
    0 installs
34. ▌
    Vendor File Format Specification Handling 2 · holobiomicslab

    Use when you have a raw MSI data file from an unknown or mixed set of vendors and need to apply format-specific data extraction, spectral parsing, or image reconstruction. The file extension alone must determine which parsing module (MSIGen.raw, MSIGen.D, MSIGen.baf, MSIGen.tdf, MSIGen.
    0 installs
35. ▌
    Extracted Ion Chromatogram Generation 2 · holobiomicslab

    Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .
    0 installs
36. ▌
    Collision Cross Section Model Validation 2 · holobiomicslab

    Use when after applying deimos.calibration.tunemix() to positive-mode or negative-mode tune mix data with known CCS reference compounds (m/z range typically 118–1522), verify that the resulting calibration model achieves the expected r-squared coefficient.
    0 installs
37. ▌
    Mass Spectrometry Raw Data Preprocessing 2 · holobiomicslab

    Use when when you have raw DIA mass spectrometry data files (.raw, .d, .
    0 installs
38. ▌
    Mass Spectrometry Workflow Orchestration 2 · holobiomicslab

    Use when you have a collection of mzML or mzML.gz files from LC-IMS-MS/MS experiments and need to apply a consistent, reproducible sequence of feature detection, alignment, CCS calibration, isotope detection, and MS/MS deconvolution operations across multiple samples.
    0 installs
39. ▌
    Molecular Structure Conformer Generation 2 · holobiomicslab

    Use when you have 2D molecular structures (SMILES or SDF format) and need to create 3D conformer geometries as input to subsequent computational chemistry workflows, such as CCS prediction, molecular graph construction, or voxel-based property calculations.
    0 installs
40. ▌
    Ms Ms Fragment Assignment And Annotation 3 · holobiomicslab

    Use when when you have predicted MS/MS fragments from quantum chemistry calculations on N-Me derived unsaturated sterol structures and need to map each fragment to its precursor lipid, calculate exact m/z values, estimate relative intensities, and produce a machine-readable reference table for.
    0 installs
41. ▌
    Polynomial Regression Quality Assessment 2 · holobiomicslab

    Use when after fitting a polynomial calibration model to tunemix reference data in DEIMoS, assess whether the model explains sufficient variance in the m/z–drift-time–CCS relationship.
    0 installs
42. ▌
    Spectral Feature Annotation And Labeling 2 · holobiomicslab

    Use when you have a detected feature table (m/z, drift_time, retention_time, intensity) and need to identify and label C13 isotopic clusters for singly-charged features (z=+1).
    0 installs
43. ▌
    Spectral Peak Smoothing Artifact Removal 3 · holobiomicslab

    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.
    0 installs
44. ▌
    Marker Feature Identification Chromatography Ms 3 · holobiomicslab

    Use when when processing raw chromatography–mass spectrometry data (GC–MS or LC–MS) as a 2D m/z vs retention time map and you need to identify and visualize marker features for analyte discrimination without relying on conventional peak picking.
    0 installs
45. ▌
    Mass Spectral Missing Word Fraction Computation 3 · holobiomicslab

    Use when when applying a pre-trained Spec2Vec Word2Vec model to new mass spectra (particularly those outside the model's training distribution), you need to assess whether peaks and neutral losses in query spectra have been seen during model training.
    0 installs
46. ▌
    Mass Spectral Similarity Scoring Across Samples 2 · holobiomicslab

    Use when after XCMS feature detection, grouping, and retention time correction when you have aligned features with consistent retention times and intensity patterns across samples.
    0 installs
47. ▌
    Group Wise Chemical Enrichment Calculation 3 · holobiomicslab

    Use when when comparing GNPS chemical annotations across two or more groups of samples (defined by ReDU sample-information categories such as sample type, extraction method, or ionization source) where the groups contain different numbers of files.
    0 installs
48. ▌
    Interactive Spectral Visualization Emperor 3 · holobiomicslab

    Use when when you have computed PCA coordinates from chemical annotation matrices (e.
    0 installs
49. ▌
    Sodium Adduct Detection And Classification 2 · holobiomicslab

    Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in the range of ~20–25 Da (characteristic of Na adducts).
    0 installs
50. ▌
    Lc Ms Dataset Acquisition And Curation 3 · holobiomicslab

    Use when when beginning an untargeted LC-MS metabolomics study and need to assemble a cohort of mzML files for processing; particularly when establishing performance baselines across sample counts (10, 50, 100+ samples), validating reproducibility, or preparing data for publication.
    0 installs
51. ▌
    Cohort Stratified Metabolic Performance Analysis 3 · holobiomicslab

    Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR metabolomic measurements for a plasma or serum cohort, and you need to determine how processing delays impact metabolite.
    0 installs
52. ▌
    Automated Metabolite Property Computation 2 · holobiomicslab

    Use when you have ion mobility-mass spectrometry data (raw drift times, m/z values, and feature intensities) from DTIMS-MS or SLIM-based IMS-MS platforms and need to compute collision cross section values using a calibration standard (e.g., Agilent tune-mix).
    0 installs
53. ▌
    Chemical Structure Descriptor Computation 3 · holobiomicslab

    Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or molecular geometry files, and you need to train or apply a machine-learning model to predict an instrument-dependent.
    0 installs
54. ▌
    In Memory Optimization For Large Datasets 2 · holobiomicslab

    Use when you are repeatedly querying or iterating over multidimensional MS data stored in MZA HDF5 format (retention time, drift time, m/z dimensions) and profiling shows that repeated disk I/O for the same metadata or scan ranges dominates runtime.
    0 installs
55. ▌
    Ion Clustering By Retention Time And Mass 2 · holobiomicslab

    Use when your peak table contains suspected mispicked ions—ions with similar m/z and retention time that likely represent the same metabolite split across multiple features due to preprocessing errors.
    0 installs
56. ▌
    Ion Mobility Spectrometry Peak Extraction 2 · holobiomicslab

    Use when after peaks have been detected in aligned GCIMS samples using findPeaks with CWT parameters and peaks have been clustered across samples, and you need to integrate peak signals into a matrix format where each entry represents the intensity of a peak cluster in a specific sample for.
    0 installs
57. ▌
    Ionisation Method Hardware Correspondence 2 · holobiomicslab

    Use when when evaluating whether a mass spectrometry analysis platform (such as mzmine) has comprehensive module support across multiple ionisation and separation techniques (LC, GC, IMS, MALDI MS imaging), or when planning a multi-technique MS study and needing to confirm that all intended.
    0 installs
58. ▌
    Metadata Normalization And Reconciliation 2 · holobiomicslab

    Use when you have multiple CSV feature lists from different acquisition methods (e.g., LC-MS vs LC-IMS-MS) or processing software, each using different naming conventions, retention time scales, or m/z precision;
    0 installs
59. ▌
    Ms2 Spectral Deconvolution And Annotation 2 · holobiomicslab

    Use when you have acquired LC-IMS-MS/MS data (or equivalent multidimensional MS/MS acquisition) in mzML or mzML.gz format and need to disambiguate overlapping fragmentation spectra arising from co-eluting or co-drifting precursor ions.
    0 installs
60. ▌
    Msi Preprocessing Parameter Configuration 2 · holobiomicslab

    Use when you have raw line-scan MSI data (from Bruker .d/.baf, converted to .mzML, or other supported formats) and need to configure MSIGen before calling msigen() to generate image arrays.
    0 installs
61. ▌
    Tissue Specific Metabolite Quantification 3 · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from multiple tissue samples and need to identify and quantify unsaturated sterol lipids at the isomer level (distinguishing double-bond position and stereochemistry).
    0 installs
62. ▌
    Mass Spectrometry Fragmentation Pattern Modeling 2 · holobiomicslab

    Use when when building a re-usable spectral reference library for lipidomics workflows where you need to match experimental MS/MS spectra against a comprehensive theoretical fragmentation model.
    0 installs
63. ▌
    Sample Study Size Stratified Algorithm Selection 3 · holobiomicslab

    Use when when beginning mass alignment in a multi-sample LC-MS metabolomics study, before constructing the MassGrid.
    0 installs
64. ▌
    Ms1 Feature Peak Detection In Full Scan 2 · holobiomicslab

    Use when you have merged MS1 spectra (output from spectral binning/merging steps) from a full-scan FIA-MS or LC-MS acquisition and need to identify distinct molecular features before accurate mass annotation or background filtering.
    0 installs
65. ▌
    Spectral Data Normalization And Merging 2 · holobiomicslab

    Use when you have acquired multiple MS1 spectra over a defined acquisition time range (e.g., 0–30 s in FIA-MS) and need to combine them into a unified spectrum before feature detection.
    0 installs
66. ▌
    Cnn Transformer Hybrid Architecture Design 2 · holobiomicslab

    Use when when you need to detect and classify peaks in LC-MS regions of interest (ROIs) and simultaneously localize their boundaries for area integration.
    0 installs
67. ▌
    Imaging Mass Spectrometry Characterization 2 · holobiomicslab

    Use when you have raw mass spectrometry data files (mzML, NetCDF, or vendor formats) with unknown or mixed acquisition modalities, and you need to automatically determine whether the input is LC-MS, GC-MS, IMS (ion mobility spectrometry), or MS imaging (e.
    0 installs
68. ▌
    Isotopic Signature Clustering And Grouping 2 · holobiomicslab

    Use when you have a feature table (m/z, drift_time, retention_time, intensity) from LC-IMS-MS or similar multi-dimensional MS acquisition and need to (1) link isotopic variants to their monoisotopic parent features, (2) disambiguate true chemical features from noise or instrumental artifacts, or.
    0 installs
69. ▌
    Isotopic Signature Detection And Filtering 2 · holobiomicslab

    Use when after DEIMoS isotope detection has assigned potential isotopic signatures to detected features in aligned MS1 data.
    0 installs
70. ▌
    Iterative Peak Selection From Latent Space 3 · holobiomicslab

    Use when you have latent low-dimension peak features extracted by a Graph-attention autoencoder from imaging mass spectrometry (IMS) datasets, and you need to automatically identify a ranked subset of marker ions without manual inspection.
    0 installs
71. ▌
    Multidimensional Spectral Array Extraction 2 · holobiomicslab

    Use when you have multidimensional MS data (with LC and/or ion mobility dimensions) converted to MZA HDF5 format and need to retrieve raw spectral intensity and m/z values for specific scans, retention times, drift times, or mass ranges.
    0 installs
72. ▌
    Software Architecture Documentation Review 2 · holobiomicslab

    Use when you need to verify the scope and completeness of a software platform's analytical capabilities—particularly when the project claims to support multiple input modalities (e.
    0 installs
73. ▌
    Spectral Library Merging And Deduplication 2 · holobiomicslab

    Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf, NIST binary) and ionization modes (positive/negative MS/MS or EI) that need to be combined into a single.
    0 installs
74. ▌
    Vendor Proprietary Format Interoperability 2 · holobiomicslab

    Use when you have mass spectrometry raw data in a proprietary vendor format (Thermo .raw, Agilent .d with or without ion mobility, Bruker ion mobility .d, or mzML) and need to enable reproducible, language-agnostic access to multidimensional spectra (e.
    0 installs
75. ▌
    Biotransformation Rule Application To Metabolites 3 · holobiomicslab

    Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated database of biotransformation rules (e.g., from KEGG, RetroRules, or domain-specific repositories).
    0 installs
76. ▌
    Metabolomics Database Search And Formula Matching 3 · holobiomicslab

    Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time values.
    0 installs
77. ▌
    Missing Fraction Quality Filtering For Embeddings 2 · holobiomicslab

    Use when after converting MS/MS spectra to fixed-length vector representations using a pre-trained Word2Vec model (as in Spec2Vec), filter spectra before computing similarity scores to flag those where a large fraction of the observed intensity comes from peaks or neutral losses not present in the.
    0 installs
78. ▌
    Peak Intensity Normalization Weighted Aggregation 3 · holobiomicslab

    Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments without allowing a single dominant peak to overwhelm the learned word associations.
    0 installs
79. ▌
    Multiple Linear Regression Model Application 3 · holobiomicslab

    Use when when you have an observed m/z value from mass spectrometry imaging and need to annotate it with a ranked list of candidate chemical formulae. Apply this skill when the KnownSet database (2.
    0 installs
80. ▌
    Experimental Design Metadata Integration 2 · holobiomicslab

    Use when when you have LC-MS raw data and need to process it through a feature detection and quantification pipeline in KNIME, but lack a structured mapping between sample identifiers, experimental conditions, and the raw LC-MS runs.
    0 installs
81. ▌
    Nontargeted Metabolomics Data Processing 3 · holobiomicslab

    Use when you have raw LC-MS data in vendor or mzML format and need to systematically discover and extract all detectable metabolite features across the full retention time range, without predefined target lists.
    0 installs
82. ▌
    Calibration Coefficient Accuracy Assessment 2 · holobiomicslab

    Use when after applying deimos.calibration.tunemix() to positive-mode or negative-mode tune mix reference data (containing known CCS values across m/z range 118–1522), assess whether the single-field calibration model's r-squared coefficient meets the expected precision (typically ≥0.
    0 installs
83. ▌
    Chromatogram Plot Generation Retention Time 2 · holobiomicslab

    Use when you have mass spectrometry data loaded as a Pandas DataFrame with retention time and intensity columns, and you need to visualize the overall or mass-trace-specific signal intensity distribution across the chromatographic separation.
    0 installs
84. ▌
    Cross Language Data Format Interoperability 2 · holobiomicslab

    Use when you have mass spectrometry data (LC–MS/MS, ion mobility, DIA) converted to MZA format and need to read or analyze it in multiple programming languages (Python and R), or share datasets with collaborators using different environments without requiring proprietary vendor libraries or format.
    0 installs
85. ▌
    Ion Mobility Filtering And Tolerance Tuning 2 · holobiomicslab

    Use when your raw MSI dataset is acquired on an ion-mobility-enabled instrument (e.g., Bruker .baf, .tsf, or .tdf formats) and your analyte of interest has a known or experimentally determined ion mobility value (1/K0 or drift time μs).
    0 installs
86. ▌
    Isotopic Signature Validation And Filtering 2 · holobiomicslab

    Use when after isotope detection has enumerated C13 isotopologue patterns across m/z, drift time, and retention time dimensions, and you need to reduce false positives by retaining only well-populated isotopic signature clusters before annotation or export.
    0 installs
87. ▌
    Exact Mass Utilization For Compound Identification 2 · holobiomicslab

    Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query chemicals are present in your samples and retrieve their -match factors (scoring the confidence of the spectral match) and.
    0 installs
88. ▌
    Spectral Coverage And Intensity Metric Computation 2 · holobiomicslab

    Use when you have completed a ViMMS simulation run or processed real LC-MS/MS data and need to quantitatively assess whether one DDA controller (e.g., WeightedDEWController with exclusion) outperforms another (e.g., TopNController) in terms of spectral coverage and signal recovery.
    0 installs
89. ▌
    Automated Feature Extraction From Spectra 3 · holobiomicslab

    Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication, sample scoring, or comparative profiling without manual inspection.
    0 installs
90. ▌
    Feature List Harmonization Across Methods 2 · holobiomicslab

    Use when you have feature lists in CSV format originating from different acquisition methods (e.
    0 installs
91. ▌
    Mass Spectrometry Peak Intensity Encoding 3 · holobiomicslab

    Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity dimensionality while preserving spatial relationships between measurement points, or (3) apply iterative peak picking.
    0 installs
92. ▌
    File Format Identification Mass Spectrometry 2 · holobiomicslab

    Use when you have raw MS data files from one or more instrument vendors (Agilent, Bruker, Thermo Fisher, or mzML-formatted) and need to convert them to a vendor-agnostic HDF5-based storage format for downstream software development, machine learning, or cross-platform data access.
    0 installs
93. ▌
    Imaging Mass Spectrometry Ion Identification 3 · holobiomicslab

    Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for downstream spatial analysis (e.g., tissue region annotation or biomarker discovery).
    2 installs
94. ▌
    Ion Mobility Saturation Detection And Repair 3 · holobiomicslab

    Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which distorts peak shape and abundance estimates across the m/z and drift-time axes.
    0 installs
95. ▌
    Lcims Msms Data Preprocessing Peak Detection 2 · holobiomicslab

    Use when you have loaded mzML.gz or HDF5-formatted raw LC-IMS-MS/MS data and need to identify discrete peaks before feature alignment. Use it if your goal is to reduce noise, increase signal-to-noise ratio, and prepare multi-dimensional data for cross-sample feature matching and CCS calibration.
    0 installs
96. ▌
    Mass Spectrometry Reference Standard Mapping 2 · holobiomicslab

    Use when you have acquired tunemix data (positive or negative ion mode, in .h5 format) with known CCS reference values and need to construct a calibration function that will later predict CCS values for unknown analytes.
    0 installs
97. ▌
    Spectrum Preprocessing Binning Normalization 2 · holobiomicslab

    Use when when preparing raw MS/MS spectra for input to a Siamese neural network trained to predict structural similarity scores (Tanimoto).
    0 installs
98. ▌
    Sterol Structure Representation And Curation 3 · holobiomicslab

    Use when when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or collision cross section (CCS) prediction workflows.
    0 installs
99. ▌
    Scalability Extrapolation And Throughput Estimation 3 · holobiomicslab

    Use when you have a new or modified LC-MS data processing tool and need to determine whether it can handle production-scale sample cohorts (50–100+ samples) on modest hardware (single-core CPU, ≤16 GB RAM).
    0 installs
100. ▌
     Data Format Validation And Integrity Checking 2 · holobiomicslab

     Use when after converting raw Bruker .d/.baf or other proprietary mass spectrometry imaging formats using pyBaf2Sql or ProteoWizard MSConvert, or after running MSIGen's get_image_data() function.
     0 installs