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HolobiomicsLab

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1. ▌
   Generalized Additive Model Fitting · holobiomicslab

   Use when when a feature table from LC-MS metabolomic profiling contains QC (quality control) sample annotations and exhibits systematic signal drift correlated with run order or batch number.
   0 installs
2. ▌
   Genome Identifier Organism Mapping · 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
3. ▌
   Gnps Molecular Network Integration · 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
4. ▌
   Gnps Workflow Identifier Retrieval · holobiomicslab

   Use when when you have a GNPS molecular networking task ID and need to fetch the job archive, decompose it into standard metabolomics file formats (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings), and prepare them for integration with genomics data.
   2 installs
5. ▌
   Gradient Space Optimization Search · holobiomicslab

   Use when after fitting a Gaussian Process regression model to prior LC-MS gradient runs (retention times, separation efficiency scores, or compound identification counts).
   0 installs
6. ▌
   Hyperparameter Sweep Configuration · holobiomicslab

   Use when when implementing multiple competing model architectures (e.
   0 installs
7. ▌
   Instrument Metadata Classification · holobiomicslab

   Use when when preprocessing a heterogeneous spectral library (e.g., GNPS public library) that contains spectra from multiple instrument types, and you need to partition data by a single instrument class to train or evaluate a formula-prediction model.
   0 installs
8. ▌
   Ion Mobility Heatmap Visualization · holobiomicslab

   Use when you have raw LC-IMS-MS data (Agilent, Thermo, Bruker, or mzML format) and need to visualize and export the spatial distribution of a specific ion species (or ion family) across both ion mobility and retention time dimensions.
   0 installs
9. ▌
   Isf Relationship Tree Construction · holobiomicslab

   Use when after completing ISFrag Part 4 (Identification of ISF Features) when you have a validated feature table with identified ISF features and need to visualize or export the hierarchical fragmentation structure linking parent ions to their in-source fragments.
   2 installs
10. ▌
    Isotopic Enrichment Quantification · 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
11. ▌
    JSON Serialization Deserialization · holobiomicslab

    Use when when you have completed a computational step (e.g., corpus feature extraction or gensim LDA inference) and need to persist the result for later retrieval, pass it to a separate process (e.g., Celery task), or load it into a database.
    2 installs
12. ▌
    Kegg Candidate Network Integration · 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
13. ▌
    Knowledge Graph Integration Design · holobiomicslab

    Use when designing a metabolite annotation workflow that must simultaneously leverage established biochemical knowledge (pathway databases, reaction networks) and experimental evidence (mass spectrometry feature similarity, co-occurrence patterns).
    1 install
14. ▌
    Lc Hrms Data Processing Evaluation · holobiomicslab

    Use when you have processed the same set of untargeted LC/HRMS files (mzXML, mzML, or netCDF format) with two or more peak-picking tools and need to validate which tool produces higher-quality peaklists for organic small molecules.
    0 installs
15. ▌
    Lcms Peak Alignment And Annotation · holobiomicslab

    Use when you have an XCMS-processed feature set (XCMSet object) from replicate LC/MS runs comparing labeled (e.g., 13C-glucose) and unlabeled (e.g., 12C-glucose) conditions, and need to identify which features show isotope incorporation (fold-change ≥1.5, p-value <0.
    0 installs
16. ▌
    Lipid Library Format Specification · holobiomicslab

    Use when when you have curated or synthesized a set of custom lipid species (e.g., rare or organism-specific lipids, modified lipids, or synthetic standards) and need to integrate them into LipidMatch for candidate matching against your experimental MS/MS datasets.
    0 installs
17. ▌
    Mass Grid Construction And Mapping · 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
18. ▌
    Mass Spectrometry Library Curation · holobiomicslab

    Use when when preprocessing a public MS/MS spectral library (e.g., GNPS) for machine learning and you discover discrepancies between expected and observed compound counts after filtering by instrument type, or when a known instrument metadata issue (e.
    0 installs
19. ▌
    Mass Spectrometry Library Indexing · 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
20. ▌
    Mass Spectrometry Metadata Caching · holobiomicslab

    Use when you plan to perform repeated queries or filtering on MS metadata attributes (e.g., extract all MS2 spectra with collision energy > 30 eV, or collect all scans in a retention time window) across a large MZA HDF5 file.
    0 installs
21. ▌
    Mass Spectrum Embedding Generation · holobiomicslab

    Use when you have cleaned MS/MS spectra (in formats like .mgf, .msp, .
    0 installs
22. ▌
    Matrix Structure Validation And Qc · holobiomicslab

    Use when after executing memo_from_unaligned or memo_from_aligned functions to generate a MemoMatrix object from MS2 spectra or aligned feature tables.
    2 installs
23. ▌
    Metabolite Feature Extraction Xcms · holobiomicslab

    Use when you have one or multiple raw mzXML/mzML files from DDA, DIA, or full-scan LCMS analyses and need to detect, align, and quantify metabolite features across samples to create a unified feature matrix before MS2 annotation or in-source fragment analysis.
    2 installs
24. ▌
    Metabolite Library Curation Ms1 Rt · 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
25. ▌
    Metabolite Mass Lookup Preparation · holobiomicslab

    Use when when beginning an untargeted LC-MS annotation workflow, before attempting to match experimental m/z peaks to metabolite identities.
    0 installs
26. ▌
    Metabolite Set Decomposition Plage · holobiomicslab

    Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or MS2LDA Mass2Motifs) and need to identify which metabolite sets change significantly across experimental comparisons while.
    2 installs
27. ▌
    Metabolomic Feature Table Assembly · 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.
    2 installs
28. ▌
    Metabolomics Data Input Validation · holobiomicslab

    Use when when importing a tab-delimited or Sciex OS text export metabolomics dataset into mzQuality, before building the SummarizedExperiment object.
    0 installs
29. ▌
    Metabolomics Feature Preprocessing · holobiomicslab

    Use when when you have raw profile LC-MS data in .mzML format and need to prepare regions of interest (ROI) as input for a CNN-Transformer peak detection network.
    0 installs
30. ▌
    Metabolomics Scan Metadata Linking · holobiomicslab

    Use when after running a ViMMS Environment simulation with save_eval flag enabled, when you need to preserve the link between each simulated MS/MS scan in the output mzML file and its source chemical definition, fragmentation parameters, and evaluation metrics for later analysis, comparison, or.
    0 installs
31. ▌
    Modularity Optimization Clustering · holobiomicslab

    Use when after MS-DIAL peak character estimation has grouped LC-MS features into preliminary clusters based on peak shape and chromatographic similarity, and you need to select a single representative parental feature from each cluster to reduce redundancy before MS-FINDER annotation.
    0 installs
32. ▌
    Molecular Family Grouping Analysis · holobiomicslab

    Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid pathway database dependency.
    2 installs
33. ▌
    Motifdb Reference Library Querying · holobiomicslab

    Use when after Mass2Motifs have been inferred from tandem MS/MS spectra via LDA topic modeling and you need to assign putative substructure annotations to those motifs.
    0 installs
34. ▌
    Ms Ms Feature Preparation For Gnps · 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
35. ▌
    Ms Ms Similarity Metric Comparison · 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
36. ▌
    Ms Ms Spectrum Pairwise Comparison · 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
37. ▌
    Ms Spectral Similarity Calculation · 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
38. ▌
    Ms1 Feature Ranking And Extraction · holobiomicslab

    Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the gradient provided good separation across the chemical space.
    0 installs
39. ▌
    Ms2 Fragmentation Spectrum Parsing · holobiomicslab

    Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) and need to convert them into normalized, queryable spectral objects for downstream analysis such as MS2 fingerprinting, spectral similarity scoring, or sample comparison.
    2 installs
40. ▌
    Ms2 Spectral Dissimilarity Scoring · holobiomicslab

    Use when you have MS2 fragmentation spectra from multiple metabolomics samples and need to identify samples with unusual spectral profiles that may indicate novel chemistry, independent of feature abundance or annotation status.
    0 installs
41. ▌
    Msexperiment Backend Configuration · holobiomicslab

    Use when you have multiple centroided .mzML LC-MS files that need to be loaded into a unified object for targeted peak integration, and you need to distinguish QC runs from sample runs to compute per-group quality metrics (e.g., average SNR, peak correlation, area under curve per QC cohort).
    0 installs
42. ▌
    Multidimensional Scaling Embedding · holobiomicslab

    Use when after computing a pairwise sample distance matrix from aligned MS2 fingerprint vectors and you need to visualize sample relationships, clustering, or separation by group identity in 2D space.
    2 installs
43. ▌
    Multiformat Data Export To PDF CSV · holobiomicslab

    Use when you have raw MS data in vendor formats (Agilent .d, Thermo .raw, Bruker .
    0 installs
44. ▌
    Multiplexed Spectrum Decomposition · holobiomicslab

    Use when you have SWATH-MS data (mzML or vendor binary format) where precursor isolation windows intentionally capture multiple co-eluting compounds, resulting in multiplexed MS/MS spectra that contain mixed fragment ion peaks from unknown metabolites.
    0 installs
45. ▌
    Mztab Format Export And Annotation · 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.
    2 installs
46. ▌
    Neural Network Architecture Design · 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
47. ▌
    Neural Network Inference Execution · holobiomicslab

    Use when you have (1) a molecular structure input in SMILES, InChI, or chemical formula format, (2) a pretrained ICEBERG model checkpoint with fragment generation and intensity prediction weights, and (3) a goal to predict fragmentation patterns and m/z intensities for unknown compound.
    0 installs
48. ▌
    Numerical Equivalence Verification · holobiomicslab

    Use when when you have reimplemented an algorithm in a new package or optimized an existing algorithm and need to verify that the new version produces the same numerical results as the original or reference implementation.
    0 installs
49. ▌
    Peak Height Threshold Optimization · holobiomicslab

    Use when you have raw metabolomic LC-MS data processed through XCMS CentWave feature extraction and want to improve true positive feature recovery while controlling false positive rate and crash likelihood.
    0 installs
50. ▌
    Peak Property Preparation From CSV · 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
51. ▌
    Peak Selectivity Metric Evaluation · holobiomicslab

    Use when when identifying landmark peaks for retention time alignment in multi-sample LC-MS metabolomics workflows.
    0 installs
52. ▌
    Peak To Formula Assignment Mapping · holobiomicslab

    Use when when you have a fragment peak list (m/z values and intensities) from MS/MS data and need to assign candidate chemical subformulae to each peak as part of a de novo chemical formula inference pipeline.
    0 installs
53. ▌
    Precursor Fragment Pairing For Mrm · 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
54. ▌
    Precursor Mass Tolerance Filtering · 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
55. ▌
    Proprietary Data Structure Mapping · holobiomicslab

    Use when you have received raw mass spectrometry data in one of four proprietary vendor formats (Agilent '.d', Bruker ion mobility 'd', Thermo '.raw', or mzML) and need to convert it to a cross-platform, cross-language accessible format.
    0 installs
56. ▌
    Q Value Based Confidence Filtering · holobiomicslab

    Use when after loading feature identification results (e.g., from OpenSwath or other DIA search engines) when you need to display only confident peptide precursors and their chromatograms.
    2 installs
57. ▌
    Quality Control Merge Verification · holobiomicslab

    Use when after performing an inner or left join operation to combine a feature quantification table (from MZmine3) with sample metadata, and before proceeding to data cleanup, blank removal, batch correction, or statistical analyses.
    2 installs
58. ▌
    Quality Control Metric Computation · holobiomicslab

    Use when after feature integration and imputation when you have QC-annotated LC-MS feature intensity data (CSV or data frame format) with replicate QC samples.
    0 installs
59. ▌
    Quality Control Sample Designation · holobiomicslab

    Use when when importing a new batch of centroided mzML or mzXML LC-MS files into MetCohort, before any data alignment or feature detection is performed. At least one file must be designated as QC to enable ROA detection and alignment;
    0 installs
60. ▌
    Quality Control Summary Generation · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, CV, or insource) to a peak table in a chained filtering workflow.
    0 installs
61. ▌
    Reaction Flux Concordance Analysis · 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
62. ▌
    Rescore Training Data Augmentation · 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.
    2 installs
63. ▌
    Sample Batch Metadata Organization · holobiomicslab

    Use when you have tab-delimited metabolomics data with columns for aliquot identifiers, compound names, peak areas (primary and internal standard), sample type (QC, study sample, calibration), batch labels, and injection times, and need to construct a single unified object for batch correction.
    0 installs
64. ▌
    Sample Metadata Integration For Qc · holobiomicslab

    Use when when you have an aligned MemoMatrix (sample-by-feature occurrence matrix where features are MS2 peaks and neutral losses) and corresponding sample annotations (especially blank/control sample labels), and you need to exclude background-derived peaks and losses before applying visualization.
    0 installs
65. ▌
    Sample Spectrum Metadata Alignment · holobiomicslab

    Use when you have a GNPS task ID from a completed molecular networking workflow (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING on GNPS1, or classical_networking_workflow / feature_based_molecular_networking_workflow on GNPS2) and need to access the resulting spectral.
    0 installs
66. ▌
    Simulation Evaluation Data Capture · holobiomicslab

    Use when when you have simulated DDA (data-dependent acquisition) scans from a ViMMS Environment and need to (1) quantify how well the simulated acquisition matched real or reference data (via evaluation metrics), and (2) export the results as standards-compliant mzML files for comparison with.
    0 installs
67. ▌
    Spectral Feature Vector Generation · holobiomicslab

    Use when you have a collection of MS/MS spectra in standard formats (mzML, MGF) and need to perform rapid similarity search, clustering, or joint analysis across millions of spectra without repeated peptide database searches.
    0 installs
68. ▌
    Spectral Fingerprint Vectorization · holobiomicslab

    Use when you have MS2 fragmentation spectra from multiple metabolomics samples and need to compare them in a retention time-agnostic manner, especially when samples are chemically diverse, acquired with different LC methods or mass spectrometer technologies (e.
    0 installs
69. ▌
    Spectral Library Candidate Ranking · holobiomicslab

    Use when after MS2Deepscore has selected the top 2000 candidate spectra from a library based on spectral similarity, and you need to re-rank these candidates to surface the single match (either exact or analogue) rather than rely on raw spectral similarity alone.
    0 installs
70. ▌
    Spectral Library Database Querying · holobiomicslab

    Use when you have one or more MS/MS query spectra (in mzML, mgf, msp, mzxml, json, or pickled matchms format) and a pre-built spectral library stored in SQLite with precomputed MS2Deepscore embeddings.
    0 installs
71. ▌
    Spectral Library Format Conversion · 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.
    2 installs
72. ▌
    Spectral Library Msp Serialization · holobiomicslab

    Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those spectra as a reusable MSP-format spectral library for downstream identification tasks in Excalibur, Skyline, or NIST MS.
    0 installs
73. ▌
    Spectral Library Schema Validation · holobiomicslab

    Use when after harmonizing MS/MS spectra and metadata fields (compound identifiers, adduct annotations, collision energies, instrument types) to a common schema, and before exporting the spectral library to standardized formats (mzML, mzTab, or repository-native format).
    0 installs
74. ▌
    Spectral Search Logic Control Flow · holobiomicslab

    Use when when you need to understand or modify how MS2Query routes query spectra through its dual-pathway architecture, or when integrating MS2Query into another tool and need to trace how spectral similarity scores (MS2Deepscore) feed into library-match versus analogue-search branches with.
    2 installs
75. ▌
    Spectral Similarity Scoring Cosine · holobiomicslab

    Use when you have a collection of preprocessed and cleaned mass spectrometry spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to compute all-pairs or targeted spectral similarity scores to identify related spectra, perform spectral library searches, or build a similarity network.
    2 installs
76. ▌
    Spectrum Binning And Normalization · holobiomicslab

    Use when you have raw, high-resolution MS/MS spectra in mzML, mzXML, or MGF format that need to be prepared for fast similarity searching or clustering.
    0 installs
77. ▌
    Stable Isotope Labeling Proteomics · 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
78. ▌
    System Call Invocation Via System2 · holobiomicslab

    Use when you need to query or extract data from Thermo Fisher Scientific .raw files or other proprietary binary formats accessible only through a compiled external executable (e.g., RawFileReader .NET assembly). The executable returns text or structured output (e.
    0 installs
79. ▌
    Tandem Mass Spectra Interpretation · holobiomicslab

    Use when you have an unknown MS/MS spectrum (tandem mass spectrum) with a measured precursor m/z and fragment peaks, and you need to assign the most likely molecular formula and ionization adduct (e.g., [M+H]+, [M+Na]+, [M+K]+).
    2 installs
80. ▌
    Tandem Mass Spectrum Normalization · holobiomicslab

    Use when preparing tandem MS/MS datasets for cross-dataset similarity analysis or spectral matching, particularly when datasets originate from different instruments, acquisition dates, or sample preparation protocols that may introduce systematic variations in peak intensities.
    0 installs
81. ▌
    Target List Matching And Alignment · holobiomicslab

    Use when you have LC-MS data (mzML or netCDF format) and a predefined list of target metabolites with known m/z values and retention time windows that you wish to extract and quantify.
    0 installs
82. ▌
    Tensor Preprocessing Normalization · holobiomicslab

    Use when when you have raw MS/MS spectral data in the form of intensity arrays indexed by m/z values and need to feed them into the Spec2Mol encoder neural network. Apply this skill before encoder inference to ensure spectral inputs conform to the encoder's expected dimensionality and value ranges.
    1 install
83. ▌
    Threshold Based Library Validation · holobiomicslab

    Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both molecular diversity (distinct species count) and chemical classification (lipid-type category count).
    1 install
84. ▌
    Lcms Peak Detection And Alignment · holobiomicslab

    Use when you have one or more raw mzXML or mzML LCMS data files (from DDA, DIA, or fullscan acquisition) and need to extract quantitative metabolite features for multi-sample comparative analysis.
    0 installs
85. ▌
    Lcms Spectral Peak Classification · holobiomicslab

    Use when you have raw LC-MS spectral peak data (in the format provided by DOI 10.25345/C5FD2F) and need to build a classifier that can distinguish valid peaks from false positives or background noise without manual feature engineering.
    0 installs
86. ▌
    Library Analogue Search Branching · holobiomicslab

    Use when when you need to reconstruct or validate the control-flow architecture of a spectral search system that must handle both exact-match library lookups and analogue discovery in a single pass, particularly when the system uses pre-computed embeddings for efficiency and machine learning for.
    2 installs
87. ▌
    Link Graph Assembly And Traversal · holobiomicslab

    Use when after running a scoring algorithm (e.g., MetcalfScoring) on paired genomic and metabolomic datasets.
    1 install
88. ▌
    M Z Metabolite Annotation Mapping · holobiomicslab

    Use when when you have a spatial metabolomics or LC-MS dataset with detected m/z features (as a feature matrix or SpaMTP Seurat object) and need to assign metabolite identities. Specifically: you have observed m/z values, you know the ionization polarity and expected adduct form (e.
    2 installs
89. ▌
    Machine Learning Model Evaluation · holobiomicslab

    Use when you have a trained NeatMS neural network model and a labelled validation dataset of MS1 peaks (annotated as 'High_quality' or 'Low_quality'), and you need to identify the scalar probability threshold that separates true positive from false positive peak classifications in your specific.
    2 installs
90. ▌
    Mass Accuracy Tolerance Filtering · holobiomicslab

    Use when when you have a peaklist from IDSL.IPA or similar peak-picking tools (containing observed m/z and intensity values) and need to assign molecular formulas from a prioritized chemical space.
    0 installs
91. ▌
    Mass Isotopologue Adduct Grouping · holobiomicslab

    Use when after sample alignment has established consensus retention time and m/z coordinates across all samples, and you need to identify and merge peaks that represent isotopologues (e.g., ¹³C variants) or adducts (e.
    0 installs
92. ▌
    Mass Range Constraint Application · holobiomicslab

    Use when when generating a virtual chemical mixture for LC-MS/MS simulation, or when sampling molecular formulas from a metabolite database (such as HMDB), you need to restrict the sample to a specific m/z window that matches your instrument's acquisition range or your analytical focus.
    2 installs
93. ▌
    Mass Spectra Embedding Extraction · holobiomicslab

    Use when you have tandem mass spectra (MS/MS) in .msp format and need dense, chemically meaningful vector representations for library matching, similarity computation, or structural clustering. Apply this when comparing spectra across large reference databases (e.
    0 installs
94. ▌
    Mass Spectrometry Data Extraction · holobiomicslab

    Use when you have native Thermo Fisher RAW mass spectrometry files and need to extract scan-level metadata (retention time, total ion current, scan mode), MS1/MS2 peak lists with m/z and intensity arrays, or instrument/LC/MS method details for downstream computational analysis, QC, or cross-sample.
    0 installs
95. ▌
    Mass Spectrometry Data Validation · holobiomicslab

    Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and post-filter counts of spectra and fragments at each major step (TIC cutoff, intra-spectrum grouping, frequency-based labeling).
    0 installs
96. ▌
    Mass Spectrometry Database Search · holobiomicslab

    Use when you have an unknown mass spectrum (or a representative metabolite spectrum from public data) and need to identify it by comparing it against a large reference library—particularly when the database contains billions of spectra and earlier tools like MASST are too slow or resource-intensive.
    2 installs
97. ▌
    Mass Spectrometry Feature Mapping · holobiomicslab

    Use when you have (1) aligned LC-MS/MS feature quantification matrix (features × fractions with m/z and RT for each feature), (2) bioassay activity measurements across the same fractions, and (3) need to assign bioactivity values to individual molecular network nodes to identify bioactive compounds.
    0 installs
98. ▌
    Mass Spectrometry File Validation · holobiomicslab

    Use when after MSConvert has converted vendor-specific raw mass spectrometry data (ThermoFisher, Agilent, or equivalent formats) on a Linux system and before initiating analysis in MSThunder.
    0 installs
99. ▌
    Mass Spectrometry Library Ranking · holobiomicslab

    Use when you have a set of unidentified tandem mass spectra (queries) and need to identify them by matching against a curated reference library (e.g., GNPS Orbitrap dataset).
    0 installs
100. ▌
     Mass Spectrum Basepeak Extraction · holobiomicslab

     Use when when you have Thermo Fisher Scientific .raw files from Orbitrap instruments and need to build a quantitative summary of MS1 acquisition intensity dynamics across a run—specifically, the m/z and intensity of the most intense peak in each MS1 scan.
     0 installs