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HolobiomicsLab

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1. ▌
   Mzmine Quantitative Table Parsing 3 · holobiomicslab

   Use when you have LC–MS/MS data processed through MZmine2 or MZmine3 and need to construct a feature quantification table for natural product discovery pipelines (e.g., INVENTA prioritization, GNPS networking, or metabolite annotation).
   2 installs
2. ▌
   Mzml Mzxml File Format Processing 2 · holobiomicslab

   Use when your raw LC-MS data are in vendor-specific binary formats (e.g., .raw, .d, .
   0 installs
3. ▌
   Network Graph Manipulation Python 2 · holobiomicslab

   Use when you have a molecular network graph exported from GNPS (as GraphML, JSON, or adjacency format) and separate experimental data (bioassay activity matrix, feature quantification table, or MS/MS annotations) indexed by feature ID, retention time, or m/z.
   0 installs
4. ▌
   Numerical Reproducibility Testing 2 · holobiomicslab

   Use when you have instantiated a learned component (embedding layer, encoder, or transformer submodule) from a published codebase and need to verify that its forward pass produces outputs matching the original paper's implementation before integrating it into a downstream analysis pipeline.
   0 installs
5. ▌
   Peak Detection And Mass Alignment 3 · holobiomicslab

   Use when when you have raw LC-MS/MS data files (.mzML, .raw, or vendor formats) from multiple samples and need to identify reproducible molecular features across the cohort before annotation or statistical analysis.
   0 installs
6. ▌
   Peptide Spectrum Match Annotation 2 · holobiomicslab

   Use when when you have a peptide sequence, observed MS2 spectrum peaks (m/z, intensity, charge state), and need to determine which theoretical fragment ions (B and Y ions) match the observed data—particularly in stable isotope probing (SIP) experiments where peptides carry heavy isotope labels (e.
   0 installs
7. ▌
   Precursor Ion Isolation Windowing 2 · holobiomicslab

   Use when processing SWATH-MS (Sequential Windowed Acquisition of all Theoretical Mass-spectra) raw data files (mzML or vendor format) for untargeted metabolomics, specifically before attempting to deconvolute overlapping MS/MS spectra.
   0 installs
8. ▌
   Proteomics Data Format Conversion 3 · holobiomicslab

   Use when you have vendor raw files (e.g., .raw from Thermo, .d from Agilent, .wiff2 from Sciex) that need to be converted to a standard format for analysis pipelines, data sharing, or when you require the high compression rates and fast decoding provided by Aird format.
   0 installs
9. ▌
   R Package Loading And Diagnostics 2 · holobiomicslab

   Use when when deploying an R package from a non-CRAN repository (e.g., r-universe, Bioconductor, GitHub), or when verifying that a package build is reproducible and meets CRAN submission standards prior to integration into a larger analysis pipeline.
   0 installs
10. ▌
    Script Execution Time Measurement 2 · holobiomicslab

    Use when you have a set of gallery or example scripts that must run consistently across multiple backend implementations (e.g., matplotlib, Bokeh, Plotly), and you need to verify that reported execution times are accurate or detect performance changes.
    0 installs
11. ▌
    Search Results Loader Integration 2 · holobiomicslab

    Use when you have search result files from one or more DIA-MS analysis tools and need to load them into a unified environment for Q-value filtering, cross-tool comparison (upset plots), and interactive visualization of identifications, quantifications, and coefficient of variation metrics across.
    0 installs
12. ▌
    Signal Noise Trade Off Evaluation 2 · holobiomicslab

    Use when after generating consensus spectra with fragment recurrence frequencies, when you have replicate MS/MS spectra for features and need to choose a single frequency cutoff for denoising. Triggers include: (1) uncertainty about which frequency threshold to apply across all features;
    0 installs
13. ▌
    Software Component Identification 2 · holobiomicslab

    Use when when you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions.
    0 installs
14. ▌
    Structural Annotation Integration 2 · holobiomicslab

    Use when you have structural candidates from in silico tools (SIRIUS/CANOPUS) and library spectral matches from GNPS, but need to resolve conflicting or incomplete chemical classifications into a unified consensus.
    0 installs
15. ▌
    System Library Dependency Mapping 2 · holobiomicslab

    Use when a Shiny application or similar cross-platform tool is restricted to a single operating system (e.
    0 installs
16. ▌
    Taxonomic Weighting In Annotation 2 · holobiomicslab

    Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) and MS/MS spectra, and you know the organism or taxon of origin for your samples.
    0 installs
17. ▌
    Test Result Parsing And Reporting 2 · holobiomicslab

    Use when when you need to validate that a package's periodic integration test suite (distinct from unit tests) passes as expected, or when you must collect and communicate structured evidence of test outcomes across multiple test cases.
    0 installs
18. ▌
    Topn Acquisition Parameter Tuning 2 · holobiomicslab

    Use when when you have real LC-MS/MS data (mzML format) from an untargeted metabolomics experiment and want to test how variations in TopN DDA parameters affect which precursor ions are selected and fragmented, before deploying the optimized strategy on physical instruments.
    0 installs
19. ▌
    Transformation Product Prediction 3 · holobiomicslab

    Use when after parent chemical suspects have been identified in a non-target screening workflow, use this skill when you need to screen for downstream products formed by chemical or biological transformation.
    0 installs
20. ▌
    Unit Testing Conditional Branches 2 · holobiomicslab

    Use when when implementing or refactoring a FileInterface._open method or similar polymorphic dispatcher that conditionally instantiates different handler classes based on file extension (e.g., .gz, .db) or format metadata (e.g., indexed gzip detection).
    0 installs
21. ▌
    Usi String Parsing And Resolution 2 · holobiomicslab

    Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire dataset file.
    0 installs
22. ▌
    Validated Link Ranking Comparison 2 · holobiomicslab

    Use when when you have computed multiple independent scoring functions (e.
    0 installs
23. ▌
    Virtual Environment Configuration 2 · holobiomicslab

    Use when you have a Python application (e.g., ROIAL-NMR) with documented dependencies and version constraints, and you need to install it on a fresh machine or verify that the environment can be reconstructed without import or runtime errors.
    0 installs
24. ▌
    Xcms Ramclustr Object Integration 2 · holobiomicslab

    Use when you have centroid-mode LC–MS all-ion fragmentation (AIF) data already processed through xcms for feature detection and retention-time correction, and a corresponding RamClustR object that groups co-eluting fragment ions into putative spectral clusters.
    0 installs
25. ▌
    Ccs Prediction Model Training 2 · holobiomicslab

    Use when you have a dataset of SMILES strings with corresponding experimental CCS measurements and want to build a predictive model that can rapidly generate CCS values for new molecules without running expensive ion-mobility spectrometry experiments.
    0 installs
26. ▌
    Hdf5 File Structure Traversal 2 · holobiomicslab

    Use when when you have converted multidimensional mass spectrometry data (or other complex data) into MZA HDF5 format and need to understand the file hierarchy, validate the conversion output, extract metadata tables and array structure, or access spectra across different programming environments.
    0 installs
27. ▌
    Data Format Compliance Checking 2 · holobiomicslab

    Use when mSMetaEnhancer fetches metadata from external services (CIR, CTS, PubChem, IDSM, BridgeDb) and must write enriched annotations (SMILES, InChI, CAS numbers, formulas, inchikeys, IUPAC names) into .msp files.
    0 installs
28. ▌
    HTTP File Upload Implementation 2 · holobiomicslab

    Use when you are building the initial data ingestion step of a high-throughput MS platform and need to accept raw MS files from users or instruments via a web interface. Use this skill when you require automated validation of vendor-specific formats (Thermo .
    0 installs
29. ▌
    Mass Difference Adduct Matching 2 · holobiomicslab

    Use when after correlation-based feature pairing has identified feature groups with matching temporal intensity profiles through direct-injection or plasma ionization mass spectrometry experiments. You have a set of putative feature-pair candidates and need to assign specific chemical identities (e.
    0 installs
30. ▌
    Mass Tolerance Window Filtering 2 · holobiomicslab

    Use when after calculating neutral mass from observed m/z and adduct type, and before ranking candidates by chemical plausibility. Use it whenever querying a formula database (KEGG, PubChem, or custom) to retrieve all molecular formulae within a specified mass tolerance window of each neutral mass.
    0 installs
31. ▌
    Metabolite Database Integration 2 · holobiomicslab

    Use when you need to construct a reference metabolomics database from scratch or when existing public databases (HMDB, MassBank, METLIN) need to be merged into a single queryable resource for metabolite annotation in untargeted mass spectrometry analysis.
    0 installs
32. ▌
    Metabolite Feature M Z Matching 2 · holobiomicslab

    Use when you have (1) a benchmark dataset of known molecules with accurate m/z values, retention time boundaries, and isotopologue identifiers for all enviPat-predicted adducts;
    0 installs
33. ▌
    Numeric Variable Range Analysis 2 · holobiomicslab

    Use when you have loaded a numeric column (e.g., H/C ratio, O/C ratio, m/z value, or intensity) from a CSV file into Punc'data and need to render a histogram with appropriate bar spacing. The skill is triggered when the range of the column is small enough that default bin widths (1.
    0 installs
34. ▌
    Parameter Conditional Execution 2 · holobiomicslab

    Use when when a post-processing step (such as dereplication) risks removing true positive signals due to overly strict thresholds, and you need the option to retain raw or unfiltered output without code branching.
    0 installs
35. ▌
    Pathway Robustness Benchmarking 2 · holobiomicslab

    Use when when selecting a pathway analysis method for metabolomics peak data where noise and missing peaks are prevalent, or when validating that a chosen method performs consistently across realistic data quality variations.
    0 installs
36. ▌
    Record Filtering By Field Value 2 · holobiomicslab

    Use when when you have a table of JSON records and need to select a subset matching a specific condition—for example, filtering records where 'status=active' before building a string value, or filtering 'experiment_type=MS' before constructing a matrix of dictionary objects.
    0 installs
37. ▌
    Reference Compound Verification 2 · holobiomicslab

    Use when after formatting raw mass spectrometry transition data into the EISA-EXPOSOME schema (NAME, PrecursorMZ, ProductMZ, Intensity, RT, ID columns), and before exporting the final database file.
    0 installs
38. ▌
    Regex Capture Group Application 2 · holobiomicslab

    Use when when you have PSM files (output from search engines like MaxQuant, MSGFPlus, or Sage) and spectrum files in mzML or MGF format with non-trivial or inconsistent naming schemes, and you need to establish which PSMs correspond to which spectra.
    0 installs
39. ▌
    Spectrum Metadata Title Parsing 2 · holobiomicslab

    Use when when you have PSM files from a search engine (e.g., MaxQuant, MSGFPlus, Mascot) and corresponding spectrum files in mzML or MGF format, and the spectrum identifiers in both files use different naming conventions or formats.
    0 installs
40. ▌
    Thermodynamic Index Calculation 2 · holobiomicslab

    Use when after molecular formula assignment and filtering of FT-ICR MS peaks, when you have elemental composition (C, H, O, N, S, P counts) and need to characterize metabolite thermodynamic stability, degree of oxidation, aromaticity, and unsaturation to compare compound reactivity across samples.
    0 installs
41. ▌
    Metabolite Feature Organization 2 · holobiomicslab

    Use when you have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z values are features (columns), spatial spots are observations (rows), and intensities form the feature matrix.
    0 installs
42. ▌
    Batch Normalization Implementation 2 · holobiomicslab

    Use when apply batch normalization after dense hidden layers (but not the final embedding layer) in a deep neural network trained on MS/MS spectral data, particularly when the network processes high-dimensional binned spectra (9948-dimensional vectors) and you need to stabilize gradient flow across.
    0 installs
43. ▌
    Categorical Ion Status Aggregation 2 · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object when you need to understand the distribution of ions across filter status categories (passed vs. failed filters) and want to visualize or report the count and percentage composition of each status group.
    1 install
44. ▌
    Chromatographic Feature Extraction 2 · holobiomicslab

    Use when you have centroided mzML files from LC- or GC-HRMS instruments (acquired in data-dependent mode with ddMS2) and need to systematically identify chromatographic peaks, measure their mass and retention time coordinates, and quantify their intensities before applying PFAS-specific.
    0 installs
45. ▌
    Chromatographic Peak Detection Msw 3 · 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
46. ▌
    Feature Abundance Pattern Matching 2 · holobiomicslab

    Use when after initial retention-time-based feature grouping when you have groups of multiple features at similar m/z and retention time but need to determine which features actually arise from the same compound.
    0 installs
47. ▌
    Gnps Molecular Network Integration 3 · holobiomicslab

    Use when you have computed frequent fragmentation patterns from a collection of MS/MS spectra using mineMS2, and you want to focus pattern interpretation on subsets of spectra that form meaningful network components (connected groups, cliques, or high-similarity pairs) in a GNPS molecular network.
    0 installs
48. ▌
    Mass Grid Construction And Mapping 3 · holobiomicslab

    Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix. Specifically: when study size is ≤10 samples, use pairwise anchor-prioritized alignment;
    0 installs
49. ▌
    Model Metadata Schema Verification 2 · holobiomicslab

    Use when before submitting peak data or other inputs to a machine learning classification API for the first time, after a model update, or if you encounter unexpected prediction errors. It is essential when the underlying model's input names or structure may change and require code updates.
    0 installs
50. ▌
    Ms Ms Spectrum Pairwise Comparison 2 · holobiomicslab

    Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format that have been converted to low-dimensional vectors via feature hashing, and you need to identify which spectra are similar enough to cluster together.
    0 installs
51. ▌
    Neural Network Architecture Design 2 · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV from mzMine or XCMS) for LCMS data, have generated training/validation/test batches with known class imbalance, and need to train a CNN model from scratch to achieve AUC ROC > 0.9 for distinguishing true from false positive MS1 peaks.
    0 installs
52. ▌
    Pathway Ranking And Prioritization 4 · 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
53. ▌
    Reaction Flux Concordance Analysis 2 · holobiomicslab

    Use when you have computed RAS (Reaction Activity Scores) from transcriptomics and GPR rules, RPS (Reaction Propensity Scores) from intracellular metabolomics via mass-action kinetics, and flux distribution differences (FFD) from constraint-based sampling across multiple biological samples.
    0 installs
54. ▌
    Rescore Training Data Augmentation 2 · holobiomicslab

    Use when when you have TCN-predicted candidate formulas with ranked scores and need to train a Siamese rescore model to re-rank those candidates.
    0 installs
55. ▌
    Spectral Library Format Conversion 2 · holobiomicslab

    Use when when you have mass spectral libraries from multiple sources (NIST, MoNA, RIKEN, GNPS) in disparate formats (MSP, MGF, MOL folder structures) or with misaligned metadata (e.
    0 installs
56. ▌
    Binary Classifier Ablation Testing 2 · holobiomicslab

    Use when you have a trained binary molecular classifier (like BitterPredict) and want to understand which groups of chemical descriptors drive its predictions.
    0 installs
57. ▌
    Bioassay Activity Data Integration 3 · 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
58. ▌
    Chemical Structure Standardization 2 · holobiomicslab

    Use when when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
    0 installs
59. ▌
    Chromatographic Data Visualization 2 · holobiomicslab

    Use when after peak detection has been completed and a feature table has been generated in MetCohort.
    0 installs
60. ▌
    Container Networking Configuration 2 · holobiomicslab

    Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate internally—specifically when you have identified service interdependencies (e.
    0 installs
61. ▌
    Corpus Bag Of Words Representation 2 · holobiomicslab

    Use when when you have raw LC-MS/MS data in MGF format and need to prepare it for unsupervised topic modeling of metabolomics fragmentation patterns.
    0 installs
62. ▌
    Data Interchange Format Conversion 2 · holobiomicslab

    Use when you have deconvoluted or processed MS/MS spectra from SWATH-MS data that need to be (1) ingested into tools requiring open formats (e.g., spectral library matching, metabolite identification pipelines), (2) archived in public repositories, or (3) shared across different analysis platforms.
    0 installs
63. ▌
    File Format Parsing And Validation 2 · holobiomicslab

    Use when you have peak/feature tables from one or more of MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest them into LipidMatch for lipid identification. The input files are in tabular format (CSV, TSV, or Excel) and their upstream tool origin may be unknown or mixed.
    0 installs
64. ▌
    Formula Based Network Construction 2 · holobiomicslab

    Use when you have a formula-assigned dataset from FT-ICR MS (or other compound-annotated mass spectrometry) and you want to characterize molecular transformations and their co-occurrence patterns—particularly in studies of DOM reactivity, fermentation, or oxidative treatment of organic mixtures.
    0 installs
65. ▌
    Fragmentation Spectrum Ion Pairing 2 · holobiomicslab

    Use when you have two MS/MS spectra (precursor m/z and fragment ion lists) and need to identify the non-overlapping set of fragment ion alignments. Use this skill when: (1) you want to move beyond monotonic alignment to capture complex ion relationships;
    0 installs
66. ▌
    Ft Icr Ms Analysis Tool Evaluation 2 · holobiomicslab

    Use when you are evaluating or selecting FT-ICR MS software for a specific metabolomics workflow and need to assess which tools support your required analytical dimensions (e.g., Van Krevelen diagrams, PERMANOVA, thermodynamic indices, chemodiversity metrics, transformation networks).
    0 installs
67. ▌
    Genome Identifier Organism Mapping 2 · holobiomicslab

    Use when a paired omics project record contains a genome identifier field (e.g., from GenBank) but lacks the corresponding organism name, or when you need to validate that genome identifiers in bulk project records can be resolved to authoritative taxonomy.
    0 installs
68. ▌
    In Silico Fragment M Z Calculation 3 · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS or direct infusion MS/MS data and need to identify lipid species by comparing observed fragment m/z values against a library of simulated fragments. Apply this skill when your lipid library is incomplete or specialized (e.
    0 installs
69. ▌
    Inference Performance Benchmarking 2 · holobiomicslab

    Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and need to rigorously compare their held-out test performance to determine which architecture balances prediction accuracy.
    0 installs
70. ▌
    Intensity Drift Artifact Detection 2 · holobiomicslab

    Use when processing raw MS intensity tables from long measurement sequences where you observe systematic, time-dependent changes in signal magnitude (e.g., progressive increase or decrease in peak intensity across a run).
    0 installs
71. ▌
    Isotopic Enrichment Quantification 2 · holobiomicslab

    Use when you have MS2 spectra from peptides with known stable isotope enrichment (e.g., 52% ¹³C incorporation), a target peptide sequence, and you need to determine which B and Y ion fragments carry how many isotope labels at each position.
    0 installs
72. ▌
    Kegg Candidate Network Integration 2 · holobiomicslab

    Use when after cluster-based filtering has produced a set of candidate KEGG compounds for each feature cluster in untargeted LC-MS data, and you need to rank these candidates by their metabolic plausibility using network context rather than mass accuracy alone.
    0 installs
73. ▌
    Mass Spectral Component Extraction 2 · holobiomicslab

    Use when raw GC-MS data (netCDF or mzML format) contains overlapping chromatographic peaks with co-eluting ions that cannot be resolved by retention time alone.
    0 installs
74. ▌
    Mass Spectrometry Benchmark Design 2 · holobiomicslab

    Use when when claiming that one mass spectrometry processing library achieves higher throughput than competitors, or when evaluating whether a new or optimized implementation delivers the expected computational efficiency gains.
    0 installs
75. ▌
    Mass Spectrometry Feature Grouping 3 · 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
76. ▌
    Mass Spectrometry Library Indexing 2 · holobiomicslab

    Use when you have a large MS/MS experiment (mzML format) requiring lipid annotation and need to match experimental spectra against >10 million theoretical lipid fragments.
    0 installs
77. ▌
    Mass Spectrometry Library Matching 4 · 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
78. ▌
    Metabolite Library Curation Ms1 Rt 2 · holobiomicslab

    Use when when you have processed authentic standards with LC-MS in positive and negative ESI modes, converted results to .mzML format, and need to build a validated in-house reference library with MS1 m/z and RT measurements for use in untargeted metabolomics compound identification workflows.
    0 installs
79. ▌
    Metabolomic Feature Table Assembly 2 · holobiomicslab

    Use when when you have LC-MS data (mzML or netCDF format) and a pre-defined list of target metabolites (m/z, retention time, and identifiers) that you wish to extract and quantify across multiple samples, rather than performing untargeted feature discovery.
    0 installs
80. ▌
    Modulation Parameter Configuration 2 · holobiomicslab

    Use when you have a raw GCxGC-MS chromatogram in NetCDF format (.cdf file) and need to import it into R as a 2D-TIC object for preprocessing (smoothing, baseline correction, peak alignment) or multivariate analysis.
    0 installs
81. ▌
    Molecular Cheminformatics Pipeline 2 · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredict.m).
    0 installs
82. ▌
    Ms Ms Feature Preparation For Gnps 2 · holobiomicslab

    Use when you have completed LC-MS/MS data processing and feature alignment in MZmine2 or Optimus, generated a feature quantification matrix and MGF file, and now need to format these outputs for submission to GNPS to compute spectral similarity networks and retrieve node/edge tables.
    0 installs
83. ▌
    Ms Ms Similarity Metric Comparison 2 · holobiomicslab

    Use when when you have MS/MS spectra from both query compounds and a reference library and need to decide which similarity metric will maximize identification accuracy (true positive rank, precision@k) or when benchmarking a new compound identification workflow against a known-good reference.
    0 installs
84. ▌
    Ms Quantitative Analysis Standards 2 · holobiomicslab

    Use when you have raw MS intensity data paired with known-concentration calibration standard measurements, and you need to convert intensities to absolute or relative concentrations.
    0 installs
85. ▌
    Ms Spectral Similarity Calculation 2 · holobiomicslab

    Use when when comparing two or more MS/MS spectra for compound identification, library matching, or spectral validation. Triggered when raw spectral data requires quantitative similarity assessment before database lookup, or when validating that two spectra originate from the same chemical compound.
    0 installs
86. ▌
    Ms Vendor Documentation Extraction 2 · holobiomicslab

    Use when you need to determine the complete set of validated instrument/vendor and acquisition mode combinations for a mass spectrometry analysis tool, when assessing whether your specific instrument platform (vendor, model, acquisition method) is supported before committing to a workflow, or when.
    0 installs
87. ▌
    Multi Library Comparative Analysis 2 · holobiomicslab

    Use when you need to evaluate whether a newly released or candidate library (e.g., spectrum_utils v0.4.
    0 installs
88. ▌
    Multiformat Data Export To PDF CSV 3 · holobiomicslab

    Use when you have raw MS data in vendor formats (Agilent .d, Thermo .raw, Bruker .
    0 installs
89. ▌
    Multivariate Regression Comparison 2 · holobiomicslab

    Use when you have paired microbiome and metabolomic (or similar compositional) data with a new regression model and want to rigorously demonstrate its predictive advantage over alternatives (Elastic Net, Random Forest, CCA).
    0 installs
90. ▌
    Mztab Format Export And Annotation 2 · holobiomicslab

    Use when after Casanovo has generated ranked peptide sequence predictions from MS/MS spectra and you need to persist, share, or integrate the results into a proteomics data management or visualization pipeline.
    0 installs
91. ▌
    Neural Network Layer Instantiation 2 · holobiomicslab

    Use when when you have a neural network layer definition (parameters, weight initialization, embedding dimension) from a trained or pretrained model checkpoint and need to generate embeddings or activations for a new batch of chemical formulas or spectrum fragments.
    0 installs
92. ▌
    Parser Error Reporting Diagnostics 2 · holobiomicslab

    Use when when implementing or extending a DSL parser (lexer + recursive descent or LALR parser) that accepts user-authored query strings.
    0 installs
93. ▌
    Peak Property Preparation From CSV 2 · holobiomicslab

    Use when you have a CSV file containing nucleoside or peptide molecular data (formulas, identifiers, retention times, intensities) that you want to simulate as LC-MS/MS runs. Use this skill as the mandatory first step before selecting a fragmentation model and noise injector in SMITER.
    0 installs
94. ▌
    Platform Specific Code Refactoring 2 · holobiomicslab

    Use when a Shiny application or R package currently runs only on Windows and you need to enable deployment on Linux or macOS.
    0 installs
95. ▌
    Precursor Fragment Pairing For Mrm 2 · holobiomicslab

    Use when when designing a targeted lipidomics experiment and you have lipid species definitions (including chain composition and adducts) but need to configure precursor–fragment transitions for MRM or PRM acquisition on a Thermo QExactive HF, Agilent QTOF, or compatible high-resolution or.
    0 installs
96. ▌
    Precursor Mass Tolerance Filtering 2 · holobiomicslab

    Use when after cosine similarity or dot-product scoring of experimental MS/MS spectra against a reference library, when you need to eliminate matches whose precursor m/z values deviate too far from the experimental precursor m/z, thereby improving specificity of library matching before final.
    0 installs
97. ▌
    Quality Control Interval Detection 2 · holobiomicslab

    Use when when you have Sciex Multiquant TXT export files containing injection sequences from metabolomics or lipidomics studies where pooled QC samples were deliberately injected at regular intervals to monitor analytical quality.
    0 installs
98. ▌
    Quantitative Ms Data Preprocessing 2 · holobiomicslab

    Use when you have raw MS intensity tables showing systematic drift during a measurement sequence (e.g., declining or variable ion counts across a run), particularly in targeted quantification workflows where external calibration standards are available.
    0 installs
99. ▌
    Retention Time Prediction Modeling 3 · holobiomicslab

    Use when you have a set of small-molecule compounds (e.g., from MS/MS library matching or database annotation) that require retention time validation or ranking to resolve ambiguous identifications.
    0 installs
100. ▌
     Stable Isotope Labeling Proteomics 2 · holobiomicslab

     Use when when you have mass spectrometry data (MS1/MS2 scans from ThermoFisher .raw files, mzML, or MGF) from cells or organisms cultured with stable isotope-enriched substrates (e.g., 13C, 15N, 2H) at any enrichment level (natural 1.
     0 installs