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HolobiomicsLab

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1. ▌
   Interactive Workflow Validation · holobiomicslab

   Use when after automated peak detection has identified candidate peaks from LC-MS mzML files, but before exporting the final metabolite library. Use this skill when you need to: (1) optimize noise and peak-detection parameters by visualizing their effect on a representative subset of peaks;
   0 installs
2. ▌
   Isotope Mass Offset Enumeration · 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).
   2 installs
3. ▌
   Jms Compliant Database Querying · holobiomicslab

   Use when you have grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments (via khipu), and you need to assign candidate metabolite identities at Level 4 annotation depth by matching against curated reference libraries.
   0 installs
4. ▌
   Kegg Identifier To Mass Mapping · holobiomicslab

   Use when you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites. This skill must be applied before the matching stage if you are working with a KEGG database (KeggDB or sample.keggDB) and require a precomputed adduct/fragment lookup table.
   2 installs
5. ▌
   Lc Ms Data Structure Validation · holobiomicslab

   Use when before launching TARDIS peak detection on a new LC–MS dataset or target compound list. Apply this skill when you have raw MS data files in vendor formats (e.g., .raw, .d) and/or a spreadsheet-based target list (.xlsx or .
   0 installs
6. ▌
   Lc Ms Feature M Z Rt Extraction · holobiomicslab

   Use when you have preprocessed LC-MS intensity data (e.
   2 installs
7. ▌
   Lc Ms Profile Data Segmentation · holobiomicslab

   Use when you have raw profile (not centroided) LC-MS data in .mzML format and need to prepare it for automated peak detection using a trained object detection network.
   2 installs
8. ▌
   Lc Ms Retention Time Adjustment · holobiomicslab

   Use when you have centroided .mzML LC–MS data with multiple sample runs and a preliminary compound target table with theoretical or measured retention times, but you suspect the expected RT values may not align with actual retention windows in your dataset.
   0 installs
9. ▌
   Lcms Feature Table Construction · holobiomicslab

   Use when you have centroided, single-polarity mzML files from DDA LC-MS experiments and need to generate a quantitative feature table with aligned m/z and retention time coordinates, isotopic annotations, and MS2 spectra for downstream statistical or annotation analysis.
   0 installs
10. ▌
    Lda Result Database Persistence · holobiomicslab

    Use when after running gensim LDA on a corpus of MS2 fragmentation features, when you need to store the LDA results (topics, document-topic assignments, term-topic distributions) in a PostgreSQL database so they can be queried and visualized by a Django web application or other downstream consumers.
    0 installs
11. ▌
    Lipid Ontology Category Mapping · holobiomicslab

    Use when you have a list of detected lipids (e.g., from LC-MS/MS lipidomics data) with associated statistical measures (p-values, fold-changes), and you need to test whether specific lipid ontology categories (e.
    0 installs
12. ▌
    Machine Learning Model Training · 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).
    2 installs
13. ▌
    Mass Action Law Flux Prediction · holobiomicslab

    Use when when you have quantified intracellular metabolite abundances (LC-MS normalized values) from multiple samples and need to predict how differences in substrate availability translate into differences in metabolic flux for specific reactions in a constraint-based metabolic model.
    0 installs
14. ▌
    Mass Spectral Feature Alignment · holobiomicslab

    Use when when you have separate LC-MS peak tables for unlabeled (C12) and labeled (C13) isotope tracer experiments and need to identify which features correspond to the same metabolite across the two labeling conditions.
    0 installs
15. ▌
    Mass Spectrometry Data Querying · holobiomicslab

    Use when you have a directory of mzML mass spectrometry files and need to systematically identify and extract scans or peaks matching specific m/z values, retention time windows, intensity thresholds, or spectral fingerprints (e.g., product ion patterns, neutral loss signatures).
    2 installs
16. ▌
    Mass Spectrometry Scan Indexing · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs. MSn to enable level-specific filtering, (3) retrieve scan ranges or specific scan numbers for targeted spectral extraction, or (4) plan.
    2 installs
17. ▌
    Mass Spectrum Adduct Assignment · holobiomicslab

    Use when when analyzing tandem mass spectra with unknown precursor adduct identity, especially for positive-mode data containing non-protonated adducts ([M+Na]+, [M+K]+, [M+NH4]+).
    2 installs
18. ▌
    Mass Spectrum Database Matching · 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.
    1 install
19. ▌
    Mass Spectrum Semantic Encoding · holobiomicslab

    Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format) and need to identify structurally related metabolites from a reference database by computing similarity in learned semantic space rather than direct spectral matching.
    0 installs
20. ▌
    Mass2motif Substructure Mapping · holobiomicslab

    Use when you have created a GNPS molecular network (classical or feature-based workflow) and run an MS2LDA experiment on the corresponding MGF spectra, and you want to annotate network nodes with shared Mass2Motifs and chemical class information to interpret the structural basis of network.
    2 installs
21. ▌
    Metabolite Cv Ratio Calculation · holobiomicslab

    Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment. Use it to remove features that are poorly reproducible or show inconsistent signal across samples relative to instrument/technical variation.
    0 installs
22. ▌
    Metabolite Metadata Integration · holobiomicslab

    Use when when you have separate quantification data (abundance matrix), sample metadata (phenotypes, treatment groups, experimental conditions), and spectral data (MS/MS fragmentation patterns or other spectral features) that must be combined for mass spectrometry-based metabolite analysis.
    0 installs
23. ▌
    Metabolite Set Activity Scoring · holobiomicslab

    Use when when you have log2-normalized, standardized peak intensity data (rows=peaks, columns=samples) with compound annotations (peak-to-metabolite mappings via KEGG/ChEBI IDs) and need to collapse individual peak signals into pathway-level summary scores for statistical comparison across.
    0 installs
24. ▌
    Metabolomics Data Preprocessing · holobiomicslab

    Use when you have raw LC/HRMS data files in mzXML, mzML, or netCDF format and need to identify individual and aggregated aligned peaks with their retention time and m/z values before applying spectral deconvolution or chemical annotation. This is the obligatory first step when using IDSL.
    0 installs
25. ▌
    Metabolomics Peak Table Loading · holobiomicslab

    Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with sample metadata for reproducibility filtering, mispicked-ion removal, or group-based feature exclusion.
    0 installs
26. ▌
    Molecular Descriptor Extraction · holobiomicslab

    Use when you have a collection of chemical structures in SMILES format and need to create paired structure–spectrum training data for a generative model, but do not have experimental MS/MS spectra available.
    0 installs
27. ▌
    Molecular Geometry File Parsing · holobiomicslab

    Use when when you have a molecular structure in XYZ or similar coordinate format and need to initialize QCxMS2 or related workflows for EI mass spectrum calculation.
    2 installs
28. ▌
    Ms Annotation Result Validation · holobiomicslab

    Use when after running annotateRC on LC–MS AIF features with fragment libraries (e.
    0 installs
29. ▌
    Ms Modification Site Evaluation · holobiomicslab

    Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the true structure of the unknown compound (oracle mode) or a reference modification site annotation.
    0 installs
30. ▌
    Ms Ms Spectral Library Matching · holobiomicslab

    Use when you have experimental MS/MS spectra from nontargeted metabolomics data and need to assign molecular identities or identify structurally related analogs.
    0 installs
31. ▌
    Ms Spectrum Similarity Grouping · holobiomicslab

    Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to a cluster group for downstream analysis such as peptide identification or spectral library construction.
    0 installs
32. ▌
    Ms2 Peak Detection And Counting · holobiomicslab

    Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when samples were acquired using different LC methods, mass spectrometer technologies, or exhibit poor feature overlap or large.
    2 installs
33. ▌
    Ms2 Spectra Parsing And Loading · holobiomicslab

    Use when when beginning a MEMO analysis workflow with raw or unaligned MS2 spectra files and needing to extract fragmentation data and precursor information before counting MS2 peaks and neutral losses to generate sample fingerprints.
    0 installs
34. ▌
    Ms2 Spectral Feature Extraction · holobiomicslab

    Use when you have LC-MS/MS metabolomics data in MGF format and need to prepare it for Latent Dirichlet Allocation (LDA) topic modeling.
    0 installs
35. ▌
    Ms2 Spectral Similarity Scoring · holobiomicslab

    Use when after temporal intensity profile correlation and exact mass difference refinement have identified candidate ion-species pairs in direct-injection plasma ionization MS data (e.g., DBDI-MS, DBDI-FT-ICR-MS).
    0 installs
36. ▌
    Ms2 Spectrum Feature Extraction · holobiomicslab

    Use when you have DDA (data-dependent acquisition) LC-MS/MS data with MS2 spectra and want to discover metabolic features that may be missed by MS1-only peak picking, or when you need an alternative feature extraction workflow that leverages fragmentation patterns to identify true metabolite.
    0 installs
37. ▌
    Ms2 Spectrum Format Preparation · holobiomicslab

    Use when you have raw or unstructured MS2 spectral data (from untargeted tandem mass spectrometry experiments) and plan to run MS2MP inference for KEGG pathway prediction.
    0 installs
38. ▌
    Ms2lda Motif To Network Mapping · holobiomicslab

    Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered substructural motifs to support structural elucidation and chemical family interpretation.
    2 installs
39. ▌
    Multi Cell Line Rps Calculation · holobiomicslab

    Use when when you have LC-MS normalized intracellular metabolite abundance measurements for multiple cell lines and need to estimate reaction activity driven by substrate availability rather than enzyme expression alone.
    0 installs
40. ▌
    Multi Dimensional Data Encoding · holobiomicslab

    Use when you have loaded LC-MS feature tables or peak detection output containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to detect anomalies such as retention time drift, m/z shifts, or intensity loss that.
    0 installs
41. ▌
    Multi Source Spectrum Retrieval · holobiomicslab

    Use when when you have a Universal Spectrum Identifier (USI) string or collection of USI strings and need to programmatically retrieve the corresponding mass spectrometry spectrum data from one of seven supported repositories (GNPS Molecular Networking, GNPS Spectral Libraries, ProteoXchange.
    0 installs
42. ▌
    Mzml File Parsing And Ingestion · holobiomicslab

    Use when you have raw profile LC-MS data in .mzML format and need to prepare it for targeted or untargeted peak detection.
    0 installs
43. ▌
    Nearest Neighbor Index Querying · holobiomicslab

    Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by precursor m/z).
    2 installs
44. ▌
    Neural Network Encoder Freezing · holobiomicslab

    Use when when you have a pre-trained encoder (e.g., TCN spectrum encoder in FIDDLE) that has learned useful representations on a source task (e.g., MS/MS spectrum encoding), and you want to train lightweight task-specific modules (e.
    0 installs
45. ▌
    Neutral Mass Derivation From Mz · holobiomicslab

    Use when after adduct configuration is complete and before querying formula databases. Use it whenever you have m/z peak lists from mass spectrometry data and need to identify the neutral mass underlying each observed ion, particularly when multiple adduct types are active in the same experiment.
    0 installs
46. ▌
    Nextflow Pipeline Orchestration · holobiomicslab

    Use when when you have raw LC-HRMS metabolomics data in .mzML or .
    0 installs
47. ▌
    Notification Payload Formatting · holobiomicslab

    Use when when a QC check fails during an LC-MS instrument run and you need to alert users in real time.
    0 installs
48. ▌
    Object Detection Model Training · holobiomicslab

    Use when you have annotated LC-MS ROI snippets with ground-truth peak/non-peak labels and boundary coordinates (peak start/end positions), and you need to build a model that can discriminate true peaks from false peaks while precisely localizing peak boundaries for area integration in future LC-MS.
    0 installs
49. ▌
    Object State Mutation Detection · holobiomicslab

    Use when when calling filter functions (e.g., filter_mispicked_ions(), filter_group(), filter_cv()) on R6-based metabolomics data objects in the mpactr package and you need to verify whether the original object's state is preserved.
    0 installs
50. ▌
    Order Agnostic Dispatch Routing · holobiomicslab

    Use when when your untargeted LC-MS pipeline must support multiple peak-picking backends and you need to let users specify which algorithm to use (via configuration file or parameter) without hard-coding algorithm dependencies.
    0 installs
51. ▌
    Peak Quality Metric Computation · holobiomicslab

    Use when you have completed XCMS preprocessing (getEIC() and fillPeaks()) on untargeted LC-MS metabolomics data and need to assign per-peak quality scores prior to manual curation, classifier training, or downstream statistical analysis.
    2 installs
52. ▌
    Peak Table Row Count Comparison · holobiomicslab

    Use when you need to validate the reference-semantics behavior of mpactr filter functions, particularly when using copy_object=FALSE. Use it to confirm that a filtering operation (e.
    0 installs
53. ▌
    Peak Table Row Count Validation · holobiomicslab

    Use when when using mpactr filter functions (e.g., filter_mispicked_ions, filter_group, filter_cv) with R6 reference semantics and uncertain whether the copy_object parameter controls deep copying or in-place modification.
    0 installs
54. ▌
    Peakmap Heatmap Rendering Mz Rt · holobiomicslab

    Use when when you have mass spectrometry data organized in a Pandas DataFrame with m/z values, retention time (RT), and intensity measurements, and you want to visualize the joint distribution and correlation of these three dimensions to identify peaks, assess separation, and detect patterns across.
    0 installs
55. ▌
    Peptide Level Spectrum Grouping · holobiomicslab

    Use when after embedding MS/MS spectra into a 32-dimensional vector space using GLEAMS, when you need to identify and group all spectra originating from the same peptide sequence.
    1 install
56. ▌
    Per Sample Spectral Aggregation · holobiomicslab

    Use when you have raw MS2 spectra from a sample and need to collapse them into a single sample-level representation for comparison across multiple samples, particularly when samples have poor feature overlap, strong retention time shifts between LC methods, or were acquired on different mass.
    2 installs
57. ▌
    Psm Annotation And Ion Matching · holobiomicslab

    Use when when you have an MS2 scan with observed peak data (m/z, intensity, charge state), a known peptide sequence, and need to determine which observed ions correspond to B and Y fragment ions. Apply this skill particularly when working with natural abundance (1.
    2 installs
58. ▌
    Python R Data Structure Mapping · holobiomicslab

    Use when when you have mass spectrometry data in R's Spectra format but need to leverage Python libraries (matchms, spectrum_utils) for specialized operations like spectral similarity scoring, filtering, or normalization that lack native R implementations or perform better in Python.
    0 installs
59. ▌
    Python Sqlite Migration And Etl · holobiomicslab

    Use when you have MS/MS spectral library data currently stored in multiple file formats (JSON, CSV, or binary) and need to enable fast, filtered queries by metadata (e.g., precursor m/z, retention time, molecular class) without loading entire libraries into memory.
    0 installs
60. ▌
    Pytorch Tensor Shape Validation · holobiomicslab

    Use when after implementing a transformer encoder backbone with masking mechanisms in PyTorch, before training on mass spectra data.
    2 installs
61. ▌
    Random Forest Regression Tuning · holobiomicslab

    Use when your MetaboSet object contains missing values (marked as NA) in the expression matrix after quality flagging, but you need complete data for multivariate analysis.
    1 install
62. ▌
    Ranked Candidate Prioritization · holobiomicslab

    Use when you have a feature quantification table (m/z, retention time, peak areas) and candidate metabolite annotations (chemical identifiers, MS/MS spectra matches, or SIRIUS/GNPS predictions) linked to a sample organism or taxon, and you need to prioritize which candidates are most biochemically.
    2 installs
63. ▌
    Retention Order Prediction Rplc · holobiomicslab

    Use when when you have a set of small molecules (as SMILES or structures) that need to be identified or ranked by their elution order in RPLC systems with acidic pH (~2.7), and you want to assess model confidence in retention predictions.
    0 installs
64. ▌
    Retention Time Window Filtering · holobiomicslab

    Use when you have mzML/mzXML chromatogram files from Thermo, Waters, or Bruker instruments and need to extract MS1 and MS2 scans matching both a target m/z value AND a known or suspected retention time range.
    0 installs
65. ▌
    Roc Curve Auc Metric Evaluation · holobiomicslab

    Use when after training a NeatMS CNN model on labeled MS1 peaks and generating predictions on a held-out test set, compute ROC-AUC to assess whether the model achieves the target discrimination threshold (AUC ≥ 0.9) without evidence of overfitting.
    0 installs
66. ▌
    Sample Partitioning By Metadata · holobiomicslab

    Use when you have a merged MGF file (e.g., from MZmine output) containing MS/MS spectra from multiple biological or environmental samples, and you need to process each sample independently through annotation pipelines (e.
    0 installs
67. ▌
    Scikit Learn Metric Computation · holobiomicslab

    Use when you have prediction arrays (model outputs) and ground-truth label arrays from a classification task and need to compute confusion matrices, accuracy scores, or other performance metrics for visualization or quantitative evaluation.
    0 installs
68. ▌
    Separation Metric Normalization · holobiomicslab

    Use when you have extracted retention times from top MS1 features across an LC-MS run and need a single, comparable metric to evaluate how effectively a gradient spreads compounds across the chromatographic window.
    0 installs
69. ▌
    Simulation Output Serialization · holobiomicslab

    Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans, and fragmentation events in memory.
    2 installs
70. ▌
    Spectral Alignment Optimization · holobiomicslab

    Use when when you have two MS/MS fragmentation spectra (with precursor m/z values and fragment ion lists) and need to establish correspondence between their fragment ions beyond simple pairwise comparison.
    0 installs
71. ▌
    Spectral Data Format Conversion · holobiomicslab

    Use when you have raw tandem mass spectrometry data in one or more of the vendor formats (MGF, mzML, or msp) and need to apply unsupervised topic modeling (LDA-based motif discovery) or comparative fragmentation analysis.
    0 installs
72. ▌
    Spectral Data Import Validation · holobiomicslab

    Use when when you have raw mass spectrometry data in one or more of the six supported file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to transform it into matchms spectrum objects for processing, cleaning, or similarity comparisons.
    2 installs
73. ▌
    Spectral Data Normalization Tic · 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
74. ▌
    Spectral Data Quality Assurance · holobiomicslab

    Use when when importing raw mass spectrometry data in formats like mzML, mzXML, msp, MGF, or JSON and you need to ensure spectral data quality before proceeding to similarity comparisons or other downstream analyses.
    0 installs
75. ▌
    Spectral File Format Conversion · holobiomicslab

    Use when when you have a GNPS molecular networking job archive (downloaded as a .zip or compressed archive) and need to prepare metabolomics spectra and molecular family data for NPLinker integration.
    0 installs
76. ▌
    Spectral Metadata Schema Design · holobiomicslab

    Use when you are implementing a file parser or data ingestion module that must read .raw (Thermo) and .mzml files from heterogeneous LC-MS instruments and pass structured data to downstream tools (e.
    1 install
77. ▌
    Spectral Peak Fragment Matching · holobiomicslab

    Use when you have MS/MS spectral data (mzML, mzXML format) and a parent mass or molecular formula, and you need to identify the metabolite(s) responsible for the observed fragmentation pattern by scoring candidates against their theoretical fragmentation profiles.
    0 installs
78. ▌
    Spectral Precursor Peak Removal · holobiomicslab

    Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry experiment (e.g., via USI) and before intensity filtering or scaling.
    2 installs
79. ▌
    Spectral Scan Metadata Matching · holobiomicslab

    Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name, molecular weight, and annotation fields), and you need to pair each scan set with its corresponding chemical record to build.
    0 installs
80. ▌
    Spectral Similarity Computation · holobiomicslab

    Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
    0 installs
81. ▌
    Statistical Enrichment Analysis · holobiomicslab

    Use when you have ranked GCF-MF (Gene Cluster Family–Molecular Family) links using two or more independent scoring functions and a set of experimentally validated links.
    0 installs
82. ▌
    Statistical Result Reproduction · holobiomicslab

    Use when you have downloaded a Jupyter notebook from a published metabolomics workflow repository (e.
    0 installs
83. ▌
    Strain Spectrum Mapping Linkage · holobiomicslab

    Use when when you have downloaded and extracted a GNPS archive (from GNPS1 or GNPS2 workflows) and need to establish which spectral records (from spectra.mgf) were generated from which bacterial strains or samples. The file_mappings.tsv or file_mappings.
    0 installs
84. ▌
    Swath Ms Spectrum Deconvolution · holobiomicslab

    Use when you have SWATH-MS raw data (mzML or vendor format) from an untargeted metabolomics experiment and need to identify metabolites.
    0 installs
85. ▌
    Tandem Mass Spectrum Clustering · holobiomicslab

    Use when you have a large collection of tandem mass spectra (mzML, mzXML, or MGF format) and want to group similar spectra into clusters to identify redundancy, discover novel peptides or metabolites, or prepare data for downstream annotation.
    0 installs
86. ▌
    Tandem Ms Output Interpretation · holobiomicslab

    Use when you have received spectrum predictions (fragment masses and intensities) from a neural model (ICEBERG, SCARF, or similar) and need to extract structural information, rank candidate molecules, or validate predictions against experimental spectra.
    0 installs
87. ▌
    Tanimoto Similarity Computation · holobiomicslab

    Use when you have a trained MS2DeepScore neural network and a set of MS/MS spectra (52 binned peaks per spectrum after preprocessing) for which you need to compute pairwise structural similarity predictions.
    0 installs
88. ▌
    Tcn Encoder Input Preprocessing · holobiomicslab

    Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z (env[:, 0]) has been removed from the feature vector to avoid leakage of mass information into the model's learned.
    0 installs
89. ▌
    Theoretical Spectrum Generation · holobiomicslab

    Use when you have a defined set of lipid species (identified by class and fatty acid composition) and need to create a high-throughput spectral library for mass spectrometry-based lipid identification.
    0 installs
90. ▌
    Tracer Metabolite Pair Matching · holobiomicslab

    Use when you have acquired LC-MS peak tables from both unlabeled (12C) and isotope-labeled (13C) samples from a stable isotope tracing experiment, paired with sample metadata distinguishing case and control groups, and you need to systematically identify which unlabeled features correspond to.
    0 installs
91. ▌
    Transformer Input Preprocessing · holobiomicslab

    Use when preparing chemical formulae (e.g., 'C6H12O6') as inputs to a transformer-based neural network for MS/MS spectrum scoring. Use it specifically when the transformer must rank multiple candidate formulae against an observed mass spectrum and element composition constraints are important;
    0 installs
92. ▌
    Untargeted Lcms Peak Annotation · holobiomicslab

    Use when you have a peak-intensity matrix from untargeted LC-MS analysis (raw detected peaks with m/z and intensity values) and need to assign putative metabolite identities.
    0 installs
93. ▌
    Usi Spectrum Identifier Parsing · holobiomicslab

    Use when when you have a USI string (e.g., mzspec:MTBLS1124:QC07.
    0 installs
94. ▌
    Vendor Instrument Data Handling · holobiomicslab

    Use when you have acquired raw mass spectrometry data in vendor-proprietary formats (ThermoFisher, Agilent, or equivalent) and need to analyze it using MSThunder for unknown organic pollutant identification.
    0 installs
95. ▌
    Workflow Branching Logic Design · holobiomicslab

    Use when when a spectral matching tool produces mixed output containing both exact library matches and analog search results, and your analysis or publication requires separate handling, interpretation, or reporting of these two match classes.
    2 installs
96. ▌
    Chemical Shift Reference Matching · holobiomicslab

    Use when when preparing an input spectral peak list for NMRformer or similar Transformer-based peak assignment models, and you have observed peaks whose chemical shifts do not align with known metabolite signatures.
    0 installs
97. ▌
    Command Line Interface Invocation · holobiomicslab

    Use when when you have installed a Python package and need to verify that its command-line entry point is accessible, or when you need to discover available commands and options for NMR data processing workflows without consulting external documentation.
    0 installs
98. ▌
    Emd Spectral Distance Computation · holobiomicslab

    Use when you have an NMR mixture spectrum and a library of single-compound reference spectra, and you need to identify which compounds are present in the mixture and their abundances.
    0 installs
99. ▌
    Endianness Detection And Handling · holobiomicslab

    Use when when reading a binary file format with a magic integer or fixed checksum field at a known offset, and endianness is not explicitly declared in file metadata or header comments.
    0 installs
100. ▌
     Mass Spectrometry Data Processing · holobiomicslab

     Use when you have raw mass spectrometry data in vendor-specific formats (Thermo RAW, Waters RAW, or open formats like mzML/jcamp) that need to be ingested, validated, and converted to a standardized representation for downstream peak detection, quantification, or integration with other NMR/IR/MS.
     0 installs