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HolobiomicsLab

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1. ▌
   Compound Structural Fingerprint Comparison · holobiomicslab

   Use when you have a set of query chemicals and a reference library (organized by type or group), and you need to determine which reference compounds most closely resemble each query chemical based on structural features.
   0 installs
2. ▌
   Gc Ms Data Preprocessing And Normalization · holobiomicslab

   Use when you have raw GC-MS data (aroma, breath, or other volatile analyte samples) in NetCDF or vendor-native format and need to identify multivariate chemo-/biomarker features without conventional peak picking.
   2 installs
3. ▌
   Imaging Mass Spectrometry Characterization · holobiomicslab

   Use when you have raw mass spectrometry data files (mzML, NetCDF, or vendor formats) with unknown or mixed acquisition modalities, and you need to automatically determine whether the input is LC-MS, GC-MS, IMS (ion mobility spectrometry), or MS imaging (e.
   0 installs
4. ▌
   Left Censored Missing Value Classification · holobiomicslab

   Use when you have a metabolomics dataset (LC/MS or GC/MS) with missing values and need to determine which are below the limit of detection (LOD) or limit of quantification (LOQ). Left-censored classification is necessary when the missingness is informative—i.
   0 installs
5. ▌
   Metabolomics Imputation Method Application · holobiomicslab

   Use when your metabolomics dataset (LC/MS or GC/MS) contains missing values encoded as NA or zero that represent compounds below the instrument's limit of detection (LOD) or limit of quantification (LOQ), rather than values missing completely at random.
   0 installs
6. ▌
   Multi Task Attention Mechanism Integration · holobiomicslab

   Use when when baseline MLP or GNN models for spectral prediction show limited performance on metabolite annotation tasks, and you have access to auxiliary spectral topic labels (e.g., via LDA on spectral features) that could provide regularization signal.
   0 installs
7. ▌
   Software Architecture Documentation Review · holobiomicslab

   Use when you need to verify the scope and completeness of a software platform's analytical capabilities—particularly when the project claims to support multiple input modalities (e.
   0 installs
8. ▌
   Spectral Database Integration And Sampling · holobiomicslab

   Use when you need to generate synthetic LC/GC-MS feature tables or raw mzML files with realistic peak complexity, ion multiplicities, and natural spectral variation—not just theoretical m/z values.
   0 installs
9. ▌
   Spectral Library Merging And Deduplication · holobiomicslab

   Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf, NIST binary) and ionization modes (positive/negative MS/MS or EI) that need to be combined into a single.
   0 installs
10. ▌
    Spectral Vector Normalization By Intensity · holobiomicslab

    Use when when converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring. Specifically, apply this skill after you have represented individual peaks and neutral losses as words ('[redacted-email]', 'loss@xxx.
    0 installs
11. ▌
    Background Ion Drift Detection And Removal · holobiomicslab

    Use when processing MS-DIAL peak lists from untargeted LC-MS/MS experiments (DDA or DIA mode) where you suspect instrumental background contamination or ion source carry-over is generating false positive features.
    2 installs
12. ▌
    Batch Preparation Class Imbalance Handling · holobiomicslab

    Use when when you have raw mzML files and a feature table (CSV from mzMine or XCMS) with labeled peaks of unequal class sizes (e.g., fewer false positives than true positives) and plan to train a CNN classifier on the LCMS data.
    0 installs
13. ▌
    Chemical Formula Subformula Classification · holobiomicslab

    Use when you have tandem mass spectra with known molecular structures (SMILES, InChI, or chemical formula) and aim to train or evaluate a formula-level spectrum predictor.
    0 installs
14. ▌
    Chromatographic Data Structure Abstraction · holobiomicslab

    Use when when ingesting raw mass spectrometry data from multiple instrument vendors or file formats into a metabolomics processing pipeline, and you need to expose spectral and chromatographic metadata through a single, consistent interface regardless of the source format's internal structure.
    0 installs
15. ▌
    Chromatographic Profile Quality Assessment · holobiomicslab

    Use when running targeted peak detection on LC-MS data acquired with multiple overlapping m/z scan windows and observing distorted or periodically discontinuous peak profiles in EIC plots.
    0 installs
16. ▌
    Chromatographic Window Coverage Assessment · holobiomicslab

    Use when after extracting retention times from top MS1 features detected in an LC-MS run, and when you need to evaluate whether a given gradient time range (e.g., 0–30 minutes) is being used efficiently to separate compounds. Apply this skill as the objective function in gradient optimization (e.
    0 installs
17. ▌
    Classification Algorithm Tuning Validation · holobiomicslab

    Use when you have labeled training data (e.g., pqm_development with 500 peaks and 89 samples) and need to select which of multiple classification algorithms (e.g., AdaBoost, Random Forest, SVM) and their hyperparameters (e.
    0 installs
18. ▌
    Cnn Transformer Hybrid Architecture Design · holobiomicslab

    Use when when you need to detect and classify peaks in LC-MS regions of interest (ROIs) and simultaneously localize their boundaries for area integration.
    0 installs
19. ▌
    Contrastive Loss Integration With Encoders · holobiomicslab

    Use when you have a transformer encoder producing representations of tandem mass spectra and need to train it using contrastive learning with pairs of original and randomly masked spectra.
    0 installs
20. ▌
    Cross Sample Alignment Matrix Construction · holobiomicslab

    Use when you have already generated per-sample MS2 fingerprints (count vectors of MS2 peaks and neutral losses to the precursor) from matchms-processed spectra using spec2vec document representations, and you need to align these fingerprints into a single matrix to enable comparison across samples.
    2 installs
21. ▌
    Deep Learning Model Inference On Test Sets · holobiomicslab

    Use when you have a pretrained deep learning model, a reserved test set with ground-truth annotations, and need to evaluate prediction quality or generate embeddings for downstream analysis. Typical triggers: benchmarking a new model against classical baselines (e.
    0 installs
22. ▌
    Deep Learning Model Loading And Prediction · holobiomicslab

    Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert each spectrum into a learned molecular embedding vector for downstream matching against a reference database.
    2 installs
23. ▌
    Deep Learning Model Training And Inference · holobiomicslab

    Use when you have paired tandem MS/MS spectra with known molecular fingerprints, chemical formulae, or SMILES annotations, and you want to learn a generalizable model that can predict molecular properties or annotate unknown spectra by ranking candidates.
    0 installs
24. ▌
    Electronic Noise Detection In Mass Spectra · holobiomicslab

    Use when you have raw MS/MS peak lists and suspect electronic noise contamination—particularly when peaks show repeated, identical intensity values across multiple m/z entries within a single spectrum, which are rare in genuine biological spectra but common in instrument artifacts.
    2 installs
25. ▌
    Embedding Space Normalization And Geometry · holobiomicslab

    Use when when designing a Siamese or multi-branch neural architecture where two or more embedding streams (e.
    0 installs
26. ▌
    Feature Occurrence Counting Across Spectra · holobiomicslab

    Use when when you have parsed MS2 spectra from a single metabolomics sample (via matchms or similar) and need to generate a sample-level feature vector that represents the chemical composition independently of chromatographic alignment.
    2 installs
27. ▌
    Filter Criteria Composition And Validation · holobiomicslab

    Use when you are preparing to reuse public tandem MS data from MassIVE via ReDU and need to partition files by sample metadata (e.g., organism, tissue type, extraction method, ionization source, pre-MS separation) into groups for co-analysis.
    0 installs
28. ▌
    Graph Neural Network Architecture Assembly · holobiomicslab

    Use when when you have: (1) a collection of molecules represented as molecular graphs (nodes=atoms, edges=bonds with chirality/order attributes); (2) structured metadata describing experimental conditions (e.
    0 installs
29. ▌
    Hierarchical Library Data Structure Design · holobiomicslab

    Use when when building a reference library for high-throughput spectral matching against experimental MS/MS data, and you need to support millions to billions of queries per second on a standardized dataset.
    0 installs
30. ▌
    High Quality Spectral Library Benchmarking · holobiomicslab

    Use when you have a pre-trained MS/MS spectral embedding model and need to validate that it achieves strong and consistent retrieval performance on curated spectral libraries that represent real-world data quality standards.
    0 installs
31. ▌
    Inchikey Structural Similarity Computation · holobiomicslab

    Use when you have a ranked list of library candidates (top 2000 by MS2Deepscore) from MS/MS spectral matching and need to re-rank them using structural metadata to distinguish true analogues and exact matches from false positives.
    0 installs
32. ▌
    Ionization Mode And Column Mode Separation · holobiomicslab

    Use when your LC-MS peak table from MS-DIAL or similar software contains data from multiple ionization modes (positive and/or negative) and/or multiple chromatographic columns (e.
    0 installs
33. ▌
    Ionization Mode Merging And Reconciliation · holobiomicslab

    Use when you have acquired MS-DIAL peak lists in both positive and negative ionization modes on the same sample set and want to consolidate detected features across modes to avoid reporting duplicate annotations for the same molecule.
    2 installs
34. ▌
    Isotopic Signature Clustering And Grouping · holobiomicslab

    Use when you have a feature table (m/z, drift_time, retention_time, intensity) from LC-IMS-MS or similar multi-dimensional MS acquisition and need to (1) link isotopic variants to their monoisotopic parent features, (2) disambiguate true chemical features from noise or instrumental artifacts, or.
    0 installs
35. ▌
    Isotopic Signature Detection And Filtering · holobiomicslab

    Use when after DEIMoS isotope detection has assigned potential isotopic signatures to detected features in aligned MS1 data.
    0 installs
36. ▌
    Latent Dirichlet Allocation Model Training · holobiomicslab

    Use when when you have preprocessed MS/MS spectral data (filtered, noise-reduced, with neutral losses extracted) and need to discover recurring fragmentation patterns across a spectral dataset.
    0 installs
37. ▌
    Mass Spectrometry Base Peak Identification · holobiomicslab

    Use when after PuInc_seeker has identified putative incorporations in XCMS-processed LC/MS data, when you have paired unlabeled and labeled sample groups (e.
    0 installs
38. ▌
    Mass Spectrometry Data Statistical Testing · holobiomicslab

    Use when you have a normalized abundance matrix from LC-MS/MS profiling with sample class assignments (e.g., phenotypic groups, disease states, treatment conditions) and need to filter metabolic features for downstream pathway analysis or biological validation.
    0 installs
39. ▌
    Mass Spectrometry Ionization Mode Handling · holobiomicslab

    Use when when you have a feature table from LC-MS preprocessed data (e.g. from asari v1.9.2) and need to annotate ions and infer neutral mass.
    0 installs
40. ▌
    Mass Spectrometry Precursor Identification · holobiomicslab

    Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate LC-MS retention time linearity, assess method reproducibility, or establish retention time calibration curves.
    0 installs
41. ▌
    Mass To Charge Ratio Matching Against Kegg · holobiomicslab

    Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z and intensity; columns = samples) and need to assign KEGG compound identifiers to observed peaks.
    0 installs
42. ▌
    Metabolite Annotation Network Architecture · holobiomicslab

    Use when when annotating large-scale untargeted metabolomics datasets where reference library coverage is incomplete and you need to infer metabolite identities for unannotated compounds by propagating annotations from seed metabolites (database matches or prior curation) across both.
    2 installs
43. ▌
    Metabolite Candidate Ranking By Confidence · holobiomicslab

    Use when you have a set of candidate metabolites for an unknown compound detected in a liquid chromatography–mass spectrometry (LC-MS) experiment, predicted RTs from a trained DNN model, and access to calibration molecules (minimum 10) that connect your observed chromatographic method to a source.
    0 installs
44. ▌
    Metabolite Feature Intensity Normalization · holobiomicslab

    Use when after imputation and batch-effect correction (OUKS steps 3–4) have been completed on your LC-MS feature-intensity table, and before statistical hypothesis testing.
    0 installs
45. ▌
    Metabolite Fold Change Statistical Testing · holobiomicslab

    Use when you have XCMS-processed LC/MS peak data from dual-labeled (e.g., 13C) and unlabeled (12C) metabolomics samples and need to distinguish features genuinely enriched by stable isotope incorporation from noise or background variation.
    0 installs
46. ▌
    Metabolite Structural Network Construction · holobiomicslab

    Use when after MamsiStructSearch has completed structural clustering of statistically significant LC-MS features (p < 0.
    0 installs
47. ▌
    Metabolomics Feature Extraction And Export · holobiomicslab

    Use when you have raw LC-MS data (mzXML format or pre-computed feature tables from external software) and need to: (1) detect both Gaussian and non-Gaussian shaped metabolic features across multiple samples, (2) align these features across samples, and (3) export EIC chromatograms with m/z.
    0 installs
48. ▌
    Metabolomics Noise Perturbation Simulation · holobiomicslab

    Use when when benchmarking or validating a pathway analysis method (such as PALS, ORA, or GSEA) on metabolomics data, you need quantitative evidence that the method's pathway rankings remain stable despite noise and missing peaks—conditions prevalent in real LC-MS/MS datasets.
    0 installs
49. ▌
    Metadata Field Based Sample Stratification · holobiomicslab

    Use when you have a feature table and accompanying CSV metadata that includes a 'Sample Type' field (or equivalent) with entries such as 'BLANK', 'QC', 'STD', or 'Unknown'.
    0 installs
50. ▌
    Missing Value Imputation By Data Recursion · holobiomicslab

    Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to features falling below the detection limit in some samples but being present above-threshold in others.
    2 installs
51. ▌
    Modular Fragmentor Interface Configuration · holobiomicslab

    Use when you need to simulate LC-MS/MS spectra for a specific biomolecule type (peptides, modified nucleosides, or other metabolites) and must choose which fragmentation model governs how parent ions break into fragment ions.
    0 installs
52. ▌
    Ms Ms Spectral Preprocessing Noise Removal · holobiomicslab

    Use when when you have raw MS/MS spectra (from NIST, MassBank, or local acquisition) and plan to compute spectral similarity for compound identification.
    2 installs
53. ▌
    Ms Ms Spectral Preprocessing Normalization · holobiomicslab

    Use when you have paired MS/MS spectra from unknown and known metabolites with raw intensity values and need to prepare them as input for a deep-learning model that will predict structural similarity.
    0 installs
54. ▌
    Multi Head Attention Mechanism Application · holobiomicslab

    Use when you have embedded sequences of chemical formulae (tokenized and converted to dense vectors) from tandem MS/MS spectra and need to learn context-dependent representations that capture dependencies between formula tokens at multiple semantic levels.
    2 installs
55. ▌
    Multi Sample Metabolomics Data Integration · holobiomicslab

    Use when you have two or more independently processed MemoMatrix objects (each generated from a separate sample set) and your analysis goal requires direct comparison of MS2 fingerprint profiles across those samples.
    0 installs
56. ▌
    Multidimensional Spectral Array Extraction · holobiomicslab

    Use when you have multidimensional MS data (with LC and/or ion mobility dimensions) converted to MZA HDF5 format and need to retrieve raw spectral intensity and m/z values for specific scans, retention times, drift times, or mass ranges.
    0 installs
57. ▌
    Neural Network Architecture Design Spectra · holobiomicslab

    Use when you have preprocessed MS/MS spectra pairs (unknown and known metabolites) with annotated structural similarity labels, and you need to learn a generalizable model that can rank candidate structures for novel unknowns by predicting their similarity to reference compounds in a database.
    0 installs
58. ▌
    Non Targeted Preprocessing Tool Comparison · holobiomicslab

    Use when you have LC-HRMS mzML data processed by at least one non-targeted pre-processing tool (XCMS, MZmine 2, MZmine 3, MS-DIAL, OpenMS, El-MAVEN, or similar), you have access to curated retention time boundaries and molecular formulas for a set of known target compounds (ideally 30+ molecules.
    0 installs
59. ▌
    Open Modification Spectral Search Strategy · holobiomicslab

    Use when when searching an unknown query MS/MS spectrum against a large spectral library (>100k spectra) for both unmodified and modified peptides, and computational speed is critical without sacrificing sensitivity or FDR control.
    0 installs
60. ▌
    Outlier Detection Qc Sample Ratio Analysis · holobiomicslab

    Use when after building a SummarizedExperiment object from metabolomics LC-MS data with QC and Study Sample types defined, when you need to identify QC samples with aberrant Compound/Internal Standard ratios (indicating instrument drift, matrix effects, or sample degradation) and Study Samples with.
    0 installs
61. ▌
    Parent Ion Fragment Hierarchy Organization · holobiomicslab

    Use when after ISF features have been identified and annotated in Part 4 of the ISFrag workflow, and you need to represent the structural relationships among ISF features and their parent ions hierarchically.
    2 installs
62. ▌
    Positional Encoding For Spectral Sequences · holobiomicslab

    Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
    0 installs
63. ▌
    Pytorch Transformer Backbone Instantiation · holobiomicslab

    Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata (chromatographic column parameters).
    2 installs
64. ▌
    Quality Control Sample Identification Lcms · holobiomicslab

    Use when when you have XCMS-preprocessed LC-MS metabolomics data with a peak table and an accompanying covariate/metadata file that contains a 'SampleType' column, and you plan to apply QC-based quality filters (such as RSD filtering) or train classifiers for peak quality assessment.
    0 installs
65. ▌
    Reference Prediction Comparison Evaluation · holobiomicslab

    Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess whether the pipeline's predictions match the reference annotations at the required sensitivity and specificity.
    1 install
66. ▌
    Residue Position Mapping To Spectrum Peaks · holobiomicslab

    Use when when you have an MS2 spectrum (FT2 scan or mzML) with observed peak data (m/z, intensity, charge states), a peptide sequence, and need to annotate which amino acid residues generated each matched fragment ion—particularly in stable isotope labeling experiments where isotopic mass shifts.
    0 installs
67. ▌
    Retention Time Agnostic Spectral Alignment · holobiomicslab

    Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts between acquisitions, or use of different LC-MS platforms (e.g., Orbitrap vs. Q-ToF).
    2 installs
68. ▌
    Retention Time Extraction From Raw Spectra · holobiomicslab

    Use when when you have Thermo Orbitrap .raw files containing known reference peptides (e.
    2 installs
69. ▌
    Root Mean Squared Error Computation By Bin · holobiomicslab

    Use when when evaluating a regression or similarity prediction model and you need to understand whether prediction error is uniform across the outcome space or concentrated in particular ranges (e.g., low structural similarity vs. high similarity scores).
    0 installs
70. ▌
    Sample Vectorization Via Spectral Features · holobiomicslab

    Use when you have unaligned MS2 spectra from multiple metabolomics samples (in mzML, mzXML, or MGF format) and need to compare them without relying on retention time or aligned m/z features.
    1 install
71. ▌
    Sensitivity Threshold Stability Assessment · holobiomicslab

    Use when you have labeled MS/MS spectra from replicate measurements and need to determine a frequency threshold for denoising that balances competing objectives: retaining true fragment signals while removing noise.
    0 installs
72. ▌
    Silhouette Analysis Threshold Optimization · holobiomicslab

    Use when when you have a pre-computed hierarchical dendrogram from structural clustering (e.g., of LC-MS features based on m/z and retention time) and want to compare or validate the cluster assignments produced by a fixed constant-threshold method.
    0 installs
73. ▌
    Spectral Data Export And Format Conversion · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-processed metabolomics data, export spectral data when you need to share clustered spectra with external annotation software (MSFinder, Sirius), perform spectrum matching against reference databases, or prepare results for collaborative analysis.
    0 installs
74. ▌
    Spectral Feature Clustering And Comparison · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.
    0 installs
75. ▌
    Spectral Feature Extraction And Annotation · holobiomicslab

    Use when you have raw LC/MS data in mzML format and need to perform non-targeted screening to discover unknown chemical features without a predefined list of target compounds.
    0 installs
76. ▌
    Spectral Graph Construction From Fragments · holobiomicslab

    Use when after you have aligned fragment ion pairs between two MS/MS spectra using maximum weight matching and need to compute statistical significance scores for the matched pairs.
    0 installs
77. ▌
    Spectral Result Visualization Verification · holobiomicslab

    Use when after running annotateRC to generate ranked candidate annotations for LC-MS AIF features, when you need to confirm that (1) the top-ranked candidate match is chemically plausible given the observed fragment ions, (2) alternative candidate annotations exist and are correctly ranked, and (3).
    0 installs
78. ▌
    Spectral Similarity Measure Implementation · holobiomicslab

    Use when you have MSMS spectra from two or more compounds and need to identify which are structurally related. Use this skill when you want to rank spectrum pairs by similarity to discover novel analogs or validate structural assignments in untargeted metabolomics or natural products discovery.
    0 installs
79. ▌
    Spectral Structural Similarity Computation · holobiomicslab

    Use when when you have pre-trained embedding vectors (e.g., from MSBERT) for a collection of mass spectra and need to establish which spectra are chemically similar for validation, clustering, or library matching.
    0 installs
80. ▌
    Spectrum Normalization And Standardization · holobiomicslab

    Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) from one or more metabolomics samples, and you need to prepare them for MS2 fingerprint generation, similarity scoring, or cross-sample comparison.
    0 installs
81. ▌
    Spectrum Object Creation And Preprocessing · holobiomicslab

    Use when when you have raw tandem mass spectrometry peak data (m/z and intensity pairs), precursor m/z, charge state, and adduct annotation for one or more compounds, and need to construct normalized spectrum objects suitable for downstream spectral alignment, modification site prediction, or.
    0 installs
82. ▌
    Stable Isotope Labelling Feature Detection · holobiomicslab

    Use when you have XCMS-processed LC/MS peak tables from paired unlabeled (12C) and labeled (13C) metabolic samples with replicate measurements, and you want to systematically detect which features show significant enrichment in the labeled condition relative to the unlabeled control.
    0 installs
83. ▌
    Structural Cluster Annotation Metabolomics · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.g., via MB-VIP with p < 0.01 and permutation testing), when you need to consolidate multiple ionization and isotopic forms of the same metabolite into structural groups for annotation and pathway mapping.
    0 installs
84. ▌
    Retention Time Mass Correspondence Resolution · holobiomicslab

    Use when you have two LC-MS untargeted metabolomic feature tables (each containing m/z, retention time, and intensity columns) and need to establish which features in dataset A correspond to which features in dataset B, typically for comparative metabolomics, batch effect correction, or.
    0 installs
85. ▌
    Root Mean Squared Error Regression Evaluation · holobiomicslab

    Use when you have a trained regression model (e.g., a neural network or similar predictor) and a held-out test set with ground-truth continuous labels, and you need to measure whether the model's predictions match the true values.
    0 installs
86. ▌
    Spectra Object Instantiation And Manipulation · holobiomicslab

    Use when you have mass spectrometry spectral data (m/z and intensity pairs, precursor m/z, MS level, and metadata) in R memory or in a file format (mzML, mzXML, CDF, MGF, MSP), and you need to organize it into a queryable, processable object before performing spectral similarity calculations.
    0 installs
87. ▌
    Spectral Artifact Identification In Tandem Ms · holobiomicslab

    Use when you have a raw or preprocessed peak table from tandem MS/MS data (e.g., from Progenesis QI, MS-DIAL, or Bruker Metaboscape) and observe features that may represent detector artifacts, incorrectly merged/split isotopic patterns, or sample carryover contaminants (e.
    0 installs
88. ▌
    Spectral Noise Filtering And Artifact Removal · holobiomicslab

    Use when you have raw MS/MS spectra in supported formats (.mgf, .mzML, or .msp) containing both chemical signal and experimental noise, prior to structural motif discovery via topic modeling.
    0 installs
89. ▌
    Spectral Noise Synthesis Poisson Distribution · holobiomicslab

    Use when when you have clean, baseline MS/MS spectra and need to create test datasets with known noise characteristics to benchmark denoising algorithms, compare denoising search performance, or validate that electronic and chemical noise removal functions correctly identify and remove injected.
    0 installs
90. ▌
    Spectral Similarity Distance Metric Selection · holobiomicslab

    Use when when you have processed LC-MS/MS spectral data in .mgf format with feature identifiers and need to compute a pairwise similarity matrix to support interactive exploration.
    0 installs
91. ▌
    Spectrum Similarity Nearest Neighbor Indexing · holobiomicslab

    Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise distance computation is computationally prohibitive.
    0 installs
92. ▌
    Tabular Data Parsing And Structure Conversion · holobiomicslab

    Use when you have a txt or tabular export file from a liquid chromatography–mass spectrometry (LC-MS) instrument (e.g., Sciex MultiQuant > v3.0.
    0 installs
93. ▌
    Tanimoto Fingerprint Ground Truth Computation · holobiomicslab

    Use when when preparing paired MS/MS spectra for training or validation of a siamese neural network model, and you have chemical structure annotations (InChI, SMILES, or InChIKey) for each spectrum but lack pre-computed structural similarity labels.
    0 installs
94. ▌
    Targeted Dia Data Extraction From Raw Spectra · holobiomicslab

    Use when when you have raw diaPASEF mzML files, a transition list with target analytes (protein, peptide, charge state), and search results (DIA-NN, OpenSwath output) containing feature metadata (retention time, ion mobility, m/z coordinates), and you need to isolate and visualize signal for.
    0 installs
95. ▌
    Transformer Input Representation Construction · holobiomicslab

    Use when you have variable-length MS/MS peak lists (m/z arrays and intensity arrays) that must be fed into a transformer architecture for tasks like compound identification or spectral clustering.
    0 installs
96. ▌
    True Positive False Positive Rate Calculation · holobiomicslab

    Use when you have a trained NeatMS neural network model (.h5 format) and need to assess its classification performance at a specific decision threshold (e.g., 0.01) to determine what fraction of true peaks are retained (TPR) versus what fraction of incorrect peaks are incorrectly accepted (FPR).
    0 installs
97. ▌
    Variance Estimation Within And Between Groups · holobiomicslab

    Use when you have a QC-annotated LC-MS feature intensity table (CSV or data frame) with replicate QC samples and biological samples from multiple batches or run orders, and you need to assess which features maintain consistent signal intensity across technical replicates (within-group) relative to.
    0 installs
98. ▌
    Vendor Mass Spectrometry File Format Handling · holobiomicslab

    Use when you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird format for batch processing, cloud deployment, or integration with downstream analysis tools.
    0 installs
99. ▌
    Warping Function Comparison Across Algorithms · holobiomicslab

    Use when after applying two or more LC-MS alignment algorithms (such as XCMS and ncGTW) to the same dataset, use this skill to determine which produces warping functions. Specifically, apply this when: (1) you have detected or suspect misaligned features in XCMS output (e.
    0 installs
100. ▌
     Zero Value Handling In Mass Spectrometry Data · holobiomicslab

     Use when after feature detection has produced a feature table with zero and missing values (sparse abundance matrix) but before multivariate statistical analysis or annotation.
     0 installs