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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Msp File Parsing Edge Case Handling · holobiomicslab

   Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final dataset or explicitly logged with a reason for exclusion.
   0 installs
2. ▌
   Numeric Array Round Trip Validation · holobiomicslab

   Use when after implementing or modifying a numerical compression codec (such as MSNumpressCoder for m/z and intensity arrays in mass-spectrometry workflows) to verify that round-trip encode–decode cycles preserve numerical values within expected tolerance.
   0 installs
3. ▌
   Sample Information Metadata Parsing · holobiomicslab

   Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
   0 installs
4. ▌
   Adduct Ionmode Consistency Checking · holobiomicslab

   Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.
   0 installs
5. ▌
   Chemical Match Score Interpretation · holobiomicslab

   Use when when you have query chemicals identified by GC-MS (with Match.Factor values) and need to verify structural similarity against a reference chemical library to confirm compound identity or detect structural analogs (e.g., isomers or homologs).
   0 installs
6. ▌
   Compound Identifier Standardization · holobiomicslab

   Use when ingesting compound metadata from multiple sources (PubChem, DrugBank, LOTUS, Dictionary of Natural Products, DrugCentral) that lack uniform column naming, have incomplete structure information, or contain only compound names without structural data.
   0 installs
7. ▌
   Eic Similarity Correlation Analysis · holobiomicslab

   Use when after abundance-correlation-based feature group refinement when you observe that larger feature groups (particularly those with 3+ features in the same m/z–retention-time window) may contain features with different peak shapes or retention-time shifts in their EICs, or when abundance.
   0 installs
8. ▌
   File Path Resolution And Validation · holobiomicslab

   Use when when initializing a SmartPeak session from a sequence file, you need to load and validate the workflow.csv and sequence.csv files that are co-located in the session directory.
   0 installs
9. ▌
   Fragmentation Database Construction · holobiomicslab

   Use when when you have completed ORCA single-point energy calculations on interpolated reaction pathway geometries and need to convert quantum mechanical fragment energies and molecular properties into a structured fragmentation channel database suitable for automated EI mass spectrum simulation.
   0 installs
10. ▌
    Gc Ms Molecular Family Organization · holobiomicslab

    Use when after auto-deconvolution of GC-MS data has produced a table of individual deconvolved mass spectra (one per detected peak), and your goal is to group spectra into molecular families based on mass spectral similarity rather than retention time or chemical class.
    0 installs
11. ▌
    Library Spectrum Database Searching · holobiomicslab

    Use when you have an unknown electron ionization (EI) mass spectrum and need to identify the compound by comparing it against a reference library (msp file format).
    0 installs
12. ▌
    Mass Spectrometry Raw Data Encoding · holobiomicslab

    Use when you have generated or obtained a two-dimensional mass-spectrometry intensity matrix (m/z × retention time scan points) with simulated or experimental peak shapes, noise, and background, and need to encode it as a binary .
    0 installs
13. ▌
    Metabolomic Feature Table Filtering · holobiomicslab

    Use when after feature detection (e.g., Asari processing of mzML files to feature tables) but before normalization, batch correction, or annotation.
    0 installs
14. ▌
    Metabolomics Feature Table Curation · holobiomicslab

    Use when you have a raw feature table (TSV/CSV) derived from LC-MS peak detection (e.
    0 installs
15. ▌
    Metabolomics Feature Transformation · holobiomicslab

    Use when when you have a feature intensity table (samples × compounds) from targeted or non-targeted metabolomics and need to prepare it for statistical modeling or multivariate analysis.
    0 installs
16. ▌
    Orthogonal Projection Deconvolution · holobiomicslab

    Use when you have overlapped peak regions in GC-MS chromatography data (multiple components eluting within the same retention time window) and need to recover the pure mass spectra of each component and their relative concentrations.
    0 installs
17. ▌
    Rank Performance Metric Computation · holobiomicslab

    Use when when you have predictions from one or more metabolite annotation models (MLP baseline, GNN, or ESP ensemble) and need to quantify ranking performance on ESI/LC-MS test spectra.
    0 installs
18. ▌
    Spectral Match Score Interpretation · holobiomicslab

    Use when when you have GC-MS output with Match.Factor values or structural similarity scores from categorate() and need to decide which identified compounds are reliable enough to carry forward. Specifically: (1) after running GC-MS and receiving a Match.Factor column;
    0 installs
19. ▌
    Two Dimensional Ms Image Processing · holobiomicslab

    Use when you have raw GC–MS or LC–MS data represented as a two-dimensional map (m/z axis vs. retention time axis) and need to identify chemo-/biomarker features across multiple analytes simultaneously, especially when conventional peak picking produces high false-positive or false-negative rates.
    0 installs
20. ▌
    Whittaker Smoother Signal Denoising · holobiomicslab

    Use when after baseline correction (e.g., via asymmetric least squares) when raw GCxGC-MS chromatograms still contain high-frequency noise that obscures true signal structure. Use it when you need to reduce noise before peak alignment or multivariate analysis (e.
    0 installs
21. ▌
    Acquisition Method Overlap Analysis · holobiomicslab

    Use when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS, or direct infusion methods (e.
    0 installs
22. ▌
    Adduct Ion Prediction And Filtering · holobiomicslab

    Use when when annotating m/z features against a metabolite database (HMDB, Lipidmaps, etc.) and the sample preparation, ionization method, or polarity mode favors specific adduct species. For example: negative-mode LC-MS or MS imaging will preferentially generate M-H and halide adducts (M+Cl);
    0 installs
23. ▌
    Adduct Mass Matching And Clustering · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.g. via MB-VIP permutation testing) when you need to consolidate redundant measurements of the same metabolite arising from different ionisation adducts (e.g. [M+H]+, [M+Na]+, [M−H]−).
    0 installs
24. ▌
    Adduct Mass Offset Parameterization · holobiomicslab

    Use when when processing LC-MS metabolomics feature tables where adduct annotation is absent or incomplete, and you need to identify which ionization adducts are present in your mass spectrometry data.
    0 installs
25. ▌
    Mass Spectrometry Data Visualization · holobiomicslab

    Use when after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or EicSimilarityParam). Use when you need to visually confirm that grouped features belong to the same compound—i.
    0 installs
26. ▌
    Mass Spectrometry Feature Annotation · holobiomicslab

    Use when when you have peak-detected LC-MS/MS data (MGF files with MS1 and MS2 spectra, plus a feature abundance table from MZmine2) and need to assign chemical structures and molecular properties to individual MS1 features rather than relying on mass-to-charge alone.
    0 installs
27. ▌
    Mass Spectrometry Feature Clustering · holobiomicslab

    Use when after XCMS feature detection and alignment when you have a CSV-formatted feature table with m/z and retention time annotations and want to deduplicate isotopic peaks, adducts, and in-source fragments into compound-level clusters before molecular weight inference or spectral matching.
    0 installs
28. ▌
    Mass Spectrometry Metric Engineering · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to quantify file quality for automated quality control, longitudinal instrument monitoring, or training a quality prediction classifier.
    0 installs
29. ▌
    Mass Spectrometry Spectral Alignment · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally modified variant of that compound—and you need to identify which atoms in the structure likely bear the modification.
    0 installs
30. ▌
    Mass Tolerance Calibration Ppm Units · holobiomicslab

    Use when when linking statistically significant LC-MS features into structural clusters based on adduct signatures and cross-assay references (e.g., [M+H]+/[M-H]−), and you need to specify the maximum allowed deviation (in ppm) between observed m/z values and calculated neutral masses.
    0 installs
31. ▌
    Massgrid Construction And Validation · holobiomicslab

    Use when after individual mass tracks (EICs) have been extracted from each sample's mzML file and you need to create a unified, cross-sample m/z reference structure. Triggered when: (1) you have ≥2 samples in a cohort; (2) mass tracks have been binned at 0.
    0 installs
32. ▌
    Maximum Weight Matching Optimization · holobiomicslab

    Use when you have computed pairwise similarity or mass difference scores between all fragment ions across two tandem mass spectra and need to select the non-overlapping set of ion pair matches.
    0 installs
33. ▌
    Metabolite Database Embedding Lookup · holobiomicslab

    Use when when you have paired tandem MS spectra and known molecular structures (SMILES or fingerprints) and want to annotate novel spectra by retrieving similar structures from a reference database without relying on spectral database matching.
    0 installs
34. ▌
    Metabolite Network Format Conversion · holobiomicslab

    Use when after downloading GNPS molecular networking results (from GNPS1 or GNPS2 workflows), use this skill to extract and standardize the compressed archive into named, canonicalized files (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings.tsv/.
    0 installs
35. ▌
    Metabolite Quality Control Filtering · holobiomicslab

    Use when after feature extraction (Asari) has produced a full feature table from mzML data, but before normalization and annotation.
    0 installs
36. ▌
    Metabolite Quality Metric Assessment · holobiomicslab

    Use when after drift correction has been applied to a MetaboSet object, and before imputation and batch correction.
    0 installs
37. ▌
    Metabolite Stoichiometry Computation · holobiomicslab

    Use when when you have quantified intracellular metabolite abundances (LC-MS normalized values) for multiple cell lines or samples, a metabolic network model with reaction stoichiometry, and you need to predict how substrate availability translates into metabolic flux differences.
    0 installs
38. ▌
    Metabolomic Feature Table Imputation · holobiomicslab

    Use when after feature detection and peak alignment have produced a feature table with zero or missing values across samples.
    0 installs
39. ▌
    Metabolomics Data Quality Assessment · holobiomicslab

    Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to statistical analysis or functional interpretation.
    0 installs
40. ▌
    Metabolomics Feature Table Filtering · holobiomicslab

    Use when when you have a raw LC-MS peak table imported from vendor software (e.
    0 installs
41. ▌
    Metabolomics Intensity Normalization · holobiomicslab

    Use when your input is a raw metabolomics intensity matrix (compounds × samples) with known batch assignment and QC sample labels, and you observe signal drift across the analytical sequence or batch-to-batch variation.
    0 installs
42. ▌
    Metabolomics Lcms Data Preprocessing · holobiomicslab

    Use when when you have raw LC-MS metabolomics data from multiple disease groups (e.g., .mzML or .npy format files) that must be converted into a uniform, normalized feature representation before training a deep learning classifier to distinguish disease states.
    0 installs
43. ▌
    Modification Notation Interpretation · holobiomicslab

    Use when you have a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to extract the underlying peptide sequence and map modification positions to enable fragment ion annotation, mass calculation, or spectral matching.
    0 installs
44. ▌
    Molecular Formula Database Filtering · holobiomicslab

    Use when when you need to constrain a large metabolite database to a specific instrumental range (e.g., m/z 100–1000) before generating virtual chemical mixtures for LC-MS/MS simulation, or when you need to verify that a reported filtered database count can be reproduced from raw database files.
    0 installs
45. ▌
    Molecular Formula Quality Assessment · holobiomicslab

    Use when immediately after formula assignment from raw FT-ICR MS peak detection, when you have a peak intensity matrix with assigned molecular formulas and need to remove spurious or low-confidence assignments before calculating thermodynamic indices, determining compound classes, or performing.
    0 installs
46. ▌
    Molecular Network Feature Annotation · holobiomicslab

    Use when when you have both (1) a molecular network graph from GNPS with MS/MS feature nodes and edges, and (2) a quantitative bioassay matrix (fractions × bioactivity measurements) from parallel LC-MS/MS fractionation of the same sample extract.
    0 installs
47. ▌
    Molecular Network Graph Construction · holobiomicslab

    Use when after completing dereplication and cosine similarity clustering in the MolNotator pipeline, when you have merged deduplicated molecular predictions and ion annotations and need to construct the final network representation for visualization and compound identification.
    0 installs
48. ▌
    Molecular Network Graph Manipulation · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you need to embed substructural motif identifiers, confidence scores, or chemical class labels as node/edge attributes for.
    0 installs
49. ▌
    Molecular Structure Input Formatting · holobiomicslab

    Use when when you have a molecular structure in any representation (drawn structure, PDB file, common name) and need to input it into mass spectrum prediction tools like ICEBERG or SCARF, or when screening candidates from chemical databases like PubChem.
    0 installs
50. ▌
    Ms Adduct Annotation And Recognition · holobiomicslab

    Use when when processing LC-MS peak tables from isotope tracing experiments where multiple ionization adducts ([M+H]+, [M+Na]+, [M+NH4]+, etc.) and in-source fragments have generated redundant features at different m/z values that represent the same underlying metabolite.
    0 installs
51. ▌
    Ms1 Full Scan Acquisition Simulation · holobiomicslab

    Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
    0 installs
52. ▌
    Ms2 Fingerprint Distance Calculation · holobiomicslab

    Use when after MS2 fingerprints have been generated by counting MS2 peaks and neutral losses in each sample, and you have aligned them into a MemoMatrix (sample-by-fingerprint matrix).
    0 installs
53. ▌
    Msconvert Integration And Invocation · holobiomicslab

    Use when when you have vendor-format LC-MS acquisition files (Thermo .raw, Bruker .d, Sciex .ms, Agilent, Waters formats) that need to be ingested into a quality control or data processing pipeline that requires open, standardized spectral formats.
    0 installs
54. ▌
    Multi Assay Cross Linking Validation · holobiomicslab

    Use when you have statistically significant features from multiple LC-MS assays with different ionization modes (e.g., positive and negative ESI) and need to collapse redundant feature representations into single structural entities.
    0 installs
55. ▌
    Multi Dataset Integration Mzrt Space · holobiomicslab

    Use when you have multiple CSV feature tables from independent metabolomic experiments, each with RT and m/z annotations, and you need to produce a single consolidated feature matrix for comparative analysis across all samples.
    0 installs
56. ▌
    Multi Task Loss Function Formulation · holobiomicslab

    Use when when training an object detection network that must predict both discrete labels (e.g., true peak vs. false peak) and continuous coordinates (e.
    0 installs
57. ▌
    Mzml File Parsing And Roi Extraction · holobiomicslab

    Use when when you have a real mzML file from an untargeted metabolomics LC-MS/MS experiment and need to extract the chemical features it contains—either to simulate a data-dependent acquisition (DDA) strategy on those same compounds, to benchmark different fragmentation controllers, or to reproduce.
    0 installs
58. ▌
    Neural Network Architecture Training · holobiomicslab

    Use when you have a pretrained TCN spectrum encoder from formula prediction and need to train a rescoring model that ranks formula candidates by confidence. The input is a set of spectra with ground-truth formula labels and multiple candidate formulas per spectrum.
    0 installs
59. ▌
    Overfitting Detection And Prevention · holobiomicslab

    Use when when training a fresh CNN model from scratch on labeled LCMS data (e.g., MS1 peak classification in NeatMS), particularly when aiming for a specific performance target (e.g., AUC ROC > 0.9) and you need to avoid wasting compute time on redundant epochs or degrading validation performance.
    0 installs
60. ▌
    Parent Fragment Relationship Mapping · holobiomicslab

    Use when after ISF features have been identified in Part 4 of the ISFrag workflow and you need to export or visualize the hierarchical structure of detected in-source fragments relative to their parent ions.
    0 installs
61. ▌
    Parent Product Relationship Tracking · holobiomicslab

    Use when when you have applied biotransformation rules to generate candidate product structures from a set of input molecules (represented as SMILES strings) and need to document which product structures were derived from which parent structures.
    0 installs
62. ▌
    Peak Detection Threshold Application · holobiomicslab

    Use when converting raw MS/MS spectra from library files (e.g., .msp format) into structured library entries, or when annotating experimental LC–MS features against fragment databases.
    0 installs
63. ▌
    Peak Intensity Distribution Analysis · holobiomicslab

    Use when after executing feature detection and quantification on raw LC-MS data (mzML or NetCDF format) using an automated pipeline such as MetaboAnalystR 4.0, and before proceeding to downstream normalization, scaling, or functional analysis.
    0 installs
64. ▌
    Peak Quality Classifier Optimization · holobiomicslab

    Use when after calculating 12 peak-quality metrics on a development set of extracted ion chromatograms (EICs) and labeled peaks, when you need to select both the classification algorithm and its optimal hyperparameters before training a final model on held-out test data.
    0 installs
65. ▌
    Peptide Sequence Composition Parsing · holobiomicslab

    Use when you have peptide or protein sequences (as FASTA strings or text identifiers) and need to compute their mass, isotopic envelope, charge state, isoelectric point, or chromatographic retention time for MS matching, peak annotation, or property prediction.
    0 installs
66. ▌
    Peptide Spectrum Matching Evaluation · holobiomicslab

    Use when when you have a tandem mass spectrum (MSMS) with known peptide sequence and wish to assess whether enabling neutral loss annotation (e.g., NH3: −17.026549, H2O: −18.010565) increases the proportion of observed m/z peaks that can be matched to predicted fragment ions.
    0 installs
67. ▌
    Physicochemical Property Computation · holobiomicslab

    Use when you have one or more peptide or protein sequences in string format and need to calculate their mass, isotopic envelope (m/z and intensity pairs), charge state behavior, isoelectric point, or predicted chromatographic retention.
    0 installs
68. ▌
    Ppm Error Validation In Metabolomics · holobiomicslab

    Use when when annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches where the mass difference exceeds your instrumental accuracy or analysis tolerance.
    0 installs
69. ▌
    Prm Acquisition Event Identification · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is happening at regular intervals consistent with your instrument method design.
    0 installs
70. ▌
    Probability Product Kernel Denoising · holobiomicslab

    Use when you have raw MS2 spectra (m/z and intensity pairs) that you want to match against a large training dataset of annotated library spectra (e.g., GNPS), and you need to reduce noise and computational burden before applying kernel-based scoring methods such as IOKR.
    0 installs
71. ▌
    Prominence Controlled Peak Selection · holobiomicslab

    Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing prominence values and need to reduce the number of detected features while maintaining signal quality.
    0 installs
72. ▌
    Qc Reference Chromatogram Extraction · holobiomicslab

    Use when when processing a batch of LC-MS samples in mzML or mzXML format where at least one file has been designated as a quality control (QC) file, extract its TIC or BPC before performing retention time correction.
    0 installs
73. ▌
    Quality Control Threshold Validation · holobiomicslab

    Use when after executing Formation formatting on processed feature tables (output from Blueshift or Gravity modules).
    0 installs
74. ▌
    Ranked Result Extraction And Display · holobiomicslab

    Use when after running annotateRC on LC–MS AIF data when you need to inspect whether a feature has multiple plausible annotations (e.g., isobaric lipids, isomers with the same fatty-acyl chain) or when the rank-1 annotation confidence is borderline and alternatives should be evaluated.
    0 installs
75. ▌
    Retention Time Correlation Filtering · holobiomicslab

    Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts with characteristic mass shifts, neutral loss fragments) from noise or unrelated peaks.
    0 installs
76. ▌
    Retention Time Prediction Validation · holobiomicslab

    Use when after training a GNN-RT model on preprocessed molecular graph data (from Train.py) or after applying transfer learning to an in-house dataset (from Transferlearning.
    0 installs
77. ▌
    Rippp Candidate Structure Generation · holobiomicslab

    Use when after identifying precursor peptides from genome assemblies via BGC mining, when you need to enumerate the chemical space of PTM variants (lantibiotic, lassopeptide, cyanobactin, or other RiPP classes) before matching tandem mass spectra against a constructed database using Dereplicator or.
    0 installs
78. ▌
    Rsd Threshold Parameter Optimization · holobiomicslab

    Use when when preparing XCMS peak tables for quality classification and you observe that the default RSD threshold (0.3 or 30%) is either too permissive (retaining noisy EICs) or too stringent (discarding valid signals).
    0 installs
79. ▌
    Sample Centric Metabolite Annotation · holobiomicslab

    Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra) and sample-level taxonomical metadata, and you want to assign both spectral identity and predicted chemical structure to.
    0 installs
80. ▌
    Sampledata Annotation And Assignment · holobiomicslab

    Use when after loading multiple LC-MS .mzML files into an MsExperiment object using MsBackendMzR backend, when you have a documented injection sequence (e.
    0 installs
81. ▌
    Search Results Filtering And Parsing · holobiomicslab

    Use when you have loaded DIA mass spectrometry search results containing feature identification data with associated Q-value scores, and you need to restrict the analytes available in selection drop-downs to those meeting a quality cutoff (typically 1% FDR equivalent) before visualization or manual.
    0 installs
82. ▌
    Siamese Network Embedding Generation · holobiomicslab

    Use when you have preprocessed MS/MS spectra binned into 10,000 equally-sized m/z bins (10–1000 m/z range) with square-root-transformed intensities, and you need to generate 200-dimensional spectral embeddings for structural similarity prediction, visualization via dimensionality reduction (e.
    0 installs
83. ▌
    Simulation Control Loop Architecture · holobiomicslab

    Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic window selection) would perform without access to real instrument time.
    0 installs
84. ▌
    Sirius Spectral Request Construction · holobiomicslab

    Use when when you have processed LC-MS/MS data with precursor m/z, ionization mode, collision energy (if available), and fragment peak lists (m/z and intensity pairs), and need to query CSI:FingerID for molecular fingerprint predictions as part of an automated metabolite identification workflow.
    0 installs
85. ▌
    Spatial Correlation Filtering In Msi · holobiomicslab

    Use when after identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular adducts from coincidental mass matches.
    0 installs
86. ▌
    Spec2vec Model Loading And Inference · holobiomicslab

    Use when you have discovered Mass2Motifs or other fragmentation pattern representations via LDA and need to generate vector embeddings to query a reference motif database (MotifDB) for structural annotation candidates.
    0 installs
87. ▌
    Spectra Data Representation Backends · holobiomicslab

    Use when you are creating a new backend to expose MS data (m/z, intensity, retention time, and other spectral properties) from a specific storage format or data source (e.g., mzML files, SQL databases, in-memory matrices, or spectral libraries) to Spectra objects.
    0 installs
88. ▌
    Spectral Feature Chemical Assignment · holobiomicslab

    Use when you have spectral feature data annotated by both in silico structural tools (e.
    0 installs
89. ▌
    Spectral Library Annotation Matching · holobiomicslab

    Use when when you have downloaded a GNPS archive (GNPS1 or GNPS2 workflows) and need to map experimental spectra to known library compounds for annotation enrichment. Apply this skill after spectral data (spectra.
    0 installs
90. ▌
    Spectral Library Matching Annotation · holobiomicslab

    Use when you have MS2 spectral data (precursor m/z, retention time, and fragment ion patterns) from UPLC-HRMS analysis of environmental or biological samples and need to assign compound identities by comparing against known reference spectra.
    0 installs
91. ▌
    Spectral Library Matching Evaluation · holobiomicslab

    Use when you have a trained spectral embedding model (e.g., MSBERT, Spec2Vec) and need to benchmark its library matching accuracy against reference spectra on a test dataset.
    0 installs
92. ▌
    Spectral Library Similarity Matching · holobiomicslab

    Use when you have an unknown experimental mass spectrum (e.g., from liquid chromatography–mass spectrometry) and need to retrieve the most structurally similar candidate molecules from a database of millions of predicted or experimental spectra.
    0 installs
93. ▌
    Spectral Match Threshold Application · holobiomicslab

    Use when after running spectral matching (e.g., GNPS library search, SIRIUS in silico annotation) and obtaining an annotation table with confidence scores, apply threshold filtering to remove low-confidence or spurious matches before downstream analysis (e.
    0 installs
94. ▌
    Spectral Metadata Enrichment Via API · holobiomicslab

    Use when you have .msp spectrum files with minimal metadata (e.g., only compound name and mass) and need to augment them with chemical structure descriptors, identifiers, and properties from external databases.
    0 installs
95. ▌
    Spectral Peak Detection Local Maxima · holobiomicslab

    Use when you have a 1D intensity array (e.g., a single MS1 or MS2 spectrum extracted from an MZA HDF5 file) and need to identify prominent peaks with their m/z indices and heights.
    0 installs
96. ▌
    Spectral Similarity Network Building · holobiomicslab

    Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical hierarchy for comparative metabolomic analysis.
    0 installs
97. ▌
    Spectrum Filtering And Normalization · holobiomicslab

    Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or quantitative analysis.
    0 installs
98. ▌
    Spectrum Vector Similarity Searching · holobiomicslab

    Use when when clustering large collections (thousands to millions) of tandem mass spectra and you need to compute a sparse pairwise distance matrix for density-based clustering.
    0 installs
99. ▌
    Sterol Lipid Isomer Characterization · holobiomicslab

    Use when you have LC-IM-MS/MS experimental data (raw mzML or vendor format) containing signals from N-Me derived unsaturated sterol lipids and need to assign double-bond positions and stereochemistry to individual sterol isomers rather than sum compositions.
    0 installs
100. ▌
     Tandem Mass Spectra Peptide Matching · holobiomicslab

     Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and wish to identify peptidic natural products or ribosomally synthesized and post-translationally modified peptides (RiPPs) against a known structure database or custom RiPP structure database.
     0 installs