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HolobiomicsLab

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1. ▌
   Ion Type Classification And Filtering · holobiomicslab

   Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification, and you need to identify which observed peaks correspond to specific fragment ion types (e.g., only b and y ions for backbone fragmentation, or immonium ions for amino acid identification).
   0 installs
2. ▌
   Isotope Pattern And Adduct Assignment · holobiomicslab

   Use when after feature detection has produced a TSV feature table (from Asari or equivalent) containing m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
   0 installs
3. ▌
   Isotopic Pattern Mispicking Detection · holobiomicslab

   Use when you have a peak table from tandem MS preprocessing (e.g., MS-DIAL, Metaboscape) and suspect that isotopic patterns have been incorrectly split during feature detection.
   1 install
4. ▌
   Landmark Peak Selection And Filtering · holobiomicslab

   Use when when preparing mass tracks for retention-time (RT) alignment across multiple LC-MS samples.
   0 installs
5. ▌
   Lc Ms Feature Alignment Cross Dataset · holobiomicslab

   Use when you have two peak-picked, conventionally aligned LC-MS metabolomics datasets (e.
   0 installs
6. ▌
   Lipid Retention Time Rule Application · holobiomicslab

   Use when you have candidate lipid annotations from spectral library matching (e.g., XCMS + CAMERA output) with MS/MS scores, and you need to reduce false positives and predict previously unannotated lipids.
   0 installs
7. ▌
   Mass Charge Retention Time Validation · holobiomicslab

   Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity designation, perform this validation step to confirm target visibility and refine m/z and RT window parameters before running.
   2 installs
8. ▌
   Mass Error Calculation And Validation · holobiomicslab

   Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation for each matched peak to verify that the annotation adheres to your specified mass tolerance (e.g., ±10 ppm or ±0.
   0 installs
9. ▌
   Mass Range Filtering For Metabolomics · holobiomicslab

   Use when when preparing a chemical database for virtual or real MS/MS acquisition, and you need to focus on a specific m/z window (e.g., 100–1000) that matches your instrument's scan range or your metabolomics study's analytical scope.
   0 installs
10. ▌
    Mass Spectrometry Data Format Parsing · holobiomicslab

    Use when you have raw MS/MS spectra in one of the supported exchange formats (.mgf, .mzML, or .msp) and need to ingest them into an MS2LDA pipeline for unsupervised motif discovery. This skill is required before any preprocessing, filtering, or ionization-mode-specific handling can occur.
    1 install
11. ▌
    Mass Spectrometry Data Interpretation · holobiomicslab

    Use when you have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and you need to estimate the neutral mass of the parent compound.
    0 installs
12. ▌
    Mass Spectrometry Data Representation · holobiomicslab

    Use when you need to store or retrieve mass spectrometry spectra (m/z and intensity pairs) from a novel data source or storage medium (e.
    0 installs
13. ▌
    Mass Spectrometry File Format Parsing · holobiomicslab

    Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized bag-of-fragments representation for unsupervised topic modeling or substructure discovery workflows.
    0 installs
14. ▌
    Mass Spectrometry Metadata Extraction · holobiomicslab

    Use when you have peak/feature tables from one or more of MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to integrate them into a unified lipidomics workflow (e.g., LipidMatch).
    0 installs
15. ▌
    Mass Spectrometry Metadata Validation · holobiomicslab

    Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or MSNovelist web services.
    0 installs
16. ▌
    Mass Spectrometry Package Integration · holobiomicslab

    Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.
    0 installs
17. ▌
    Mass Spectrometry Peak Classification · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false positives introduced by the peak-picking algorithm.
    0 installs
18. ▌
    Mass Spectrometry Prediction Modeling · holobiomicslab

    Use when when you have a collection of compound structures in SDF format (e.
    0 installs
19. ▌
    Metabolite Abundance Drift Correction · holobiomicslab

    Use when you have a raw LCMS nontargeted metabolomics abundance table spanning multiple injections with embedded pooled technical replicate (PREF) or internal standard injections distributed across the run sequence.
    2 installs
20. ▌
    Metabolite Pathway Annotation Mapping · holobiomicslab

    Use when after peak detection and statistical association or classification analysis has identified a set of significant peaks, use this skill when you need to move from individual feature-level results (peak intensities, p-values, importance scores) to functional biological interpretation via.
    0 installs
21. ▌
    Metabologenomic Database Construction · holobiomicslab

    Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified peptides (RiPPs) by integrating genomic and mass spectrometry data.
    0 installs
22. ▌
    Metabolomic Data Structure Formatting · holobiomicslab

    Use when after peak detection in MZmine2 has produced an MGF file (containing MS1 and MS2 spectra) and a feature abundance table (CSV or BIOM), but before running q2-qemistree tree construction or any QIIME 2-based metabolomic analysis.
    0 installs
23. ▌
    Metabolomic Feature Tree Construction · holobiomicslab

    Use when when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform chemical phylogeny-based diversity analyses or meta-analyses comparing metabolomic profiles across multiple samples or.
    0 installs
24. ▌
    Metabolomics Dataset Handling Massive · holobiomicslab

    Use when you are beginning a non-targeted metabolomics analysis and need to source raw LC-MS/MS data files (in mzML or NetCDF format) that have been vetted for quality and are known to support FBMN and statistical analysis.
    0 installs
25. ▌
    Metabolomics Feature Matrix Filtering · holobiomicslab

    Use when you have an aligned MemoMatrix (sample-by-feature occurrence matrix where features are MS2 peaks and neutral losses) and need to remove background noise before applying visualization or clustering techniques (MDS/PCoA, TMAP, Heatmap).
    0 installs
26. ▌
    Metabolomics Training Set Preparation · holobiomicslab

    Use when when you have LC-MS/MS acquisitions in DDA mode and need to train a customized DNMS2Purifier model to purify chimeric MS/MS spectra specific to your experimental conditions, metabolite classes, or ionization settings.
    0 installs
27. ▌
    Metadata Harmonization Across Sources · holobiomicslab

    Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and received multiple separate output files (_microbe.html, _plant.json, _matches.tsv, _library.tsv, _datasets.tsv, _count_domain.
    0 installs
28. ▌
    Missing Pattern Generation Validation · holobiomicslab

    Use when you have a complete metabolomics data matrix (simulated or real abundance table) and need to create reproducible, controlled MNAR scenarios for evaluating imputation algorithm performance.
    0 installs
29. ▌
    Molecular Formula Parsing From Smiles · holobiomicslab

    Use when you have a query MS/MS spectrum with a SMILES string and adduct type (e.g., '[M+H]+', '[M+Na]+'), and you need to validate fragment ions against chemically plausible losses from the parent compound.
    0 installs
30. ▌
    Molecular Weight Inference Comparison · holobiomicslab

    Use when after RAMClustR clustering of XCMS-detected features and prior to final compound annotation, when you need to verify the robustness of molecular weight inference or when findMain and RAMClustR predictions are available for the same compound clusters and you want to assess concordance or.
    2 installs
31. ▌
    Mpactr Data Object Lifecycle Tracking · holobiomicslab

    Use when when chaining multiple mpactr filters on a peak table and you need to decide whether to preserve intermediate filtered objects or accept in-place mutation for memory efficiency.
    0 installs
32. ▌
    Mrm Transition Lipid Identity Mapping · holobiomicslab

    Use when after parsing raw MRM data into a transition table containing m/z values, retention times, and transition parameters.
    0 installs
33. ▌
    Msi Data Matrix Import And Validation · holobiomicslab

    Use when you have MSI intensity data exported from MSiReader, SCiLS, or Cardinal as plain-text CSV files or as Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment objects, and need to load it into R as a validated msimat object for mass difference and adduct analysis.
    0 installs
34. ▌
    Multi Group Comparison Interpretation · holobiomicslab

    Use when after performing an ANOVA-style multi-group de_design() analysis on a LipidomicsExperiment object, when you need to determine whether a categorical sample variable (e.g., Cancer Stage, SampleType, Race) significantly associates with the lipid molecular profile.
    2 installs
35. ▌
    Multi Head Attention Mechanism Design · holobiomicslab

    Use when when building a transformer-based model to process mass spectrometry data (MS/MS spectra or fingerprints) where you need the model to learn multiple independent attention patterns across spectrum features simultaneously.
    1 install
36. ▌
    Multidimensional Coordinate Alignment · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples (each containing m/z, drift_time, retention_time, and intensity measurements) and need to identify which features correspond to the same chemical compound across samples.
    0 installs
37. ▌
    Mzmine Batch Processing Configuration · holobiomicslab

    Use when you have raw metabolomics data in mzML or mzXML format and need to extract ion features, align them across samples, and produce a normalized feature table for downstream statistical or chemotaxonomic analysis.
    0 installs
38. ▌
    Natural Isotope Abundance Propagation · holobiomicslab

    Use when you have LC-MS fractional abundances of measured isotopologues (FAM) from a stable isotope labeling experiment and need to recover the true mass distribution vectors (MDV) that reflect only the contribution from the isotopic tracer. Use this skill when naturally occurring isotopes (e.
    2 installs
39. ▌
    Neural Network Threshold Optimization · holobiomicslab

    Use when after training a NeatMS neural network model on labelled peak data (High_quality, Low_quality, Noise) and you need to determine the optimal probability threshold for classifying peaks in your untargeted LCMS dataset.
    1 install
40. ▌
    Noise Filtering Threshold Application · holobiomicslab

    Use when when you have raw or centroid-mode LC-MS All-ion fragmentation (AIF) spectra and need to generate or match against ion fragment databases.
    0 installs
41. ▌
    Non Pathway Metabolite Classification · holobiomicslab

    Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other non-pathway metabolite sets) by their activity levels across experimental contrasts.
    1 install
42. ▌
    Notification Configuration Management · holobiomicslab

    Use when setting up a Rapid QC-MS monitoring job and you need to define WHERE and HOW QC-fail alerts should be sent.
    0 installs
43. ▌
    Peak Intensity Threshold Optimization · holobiomicslab

    Use when you have loaded raw mass spectrometry spectral data (in MGF, MSP, mzML, or mzXML format) and need to decide which intensity threshold(s) to use for filtering out noise and low-abundance peaks.
    0 installs
44. ▌
    Peak Picking Performance Benchmarking · holobiomicslab

    Use when when you have completed non-targeted peak picking and alignment with tools such as MZmine 2, XCMS, or MS-DIAL on LC-HRMS mzML data and need to quantify performance metrics (found peaks %, degenerated isotopologue ratio, alignment errors) by comparing against a curated benchmark of known.
    0 installs
45. ▌
    Peak Property Dictionary Construction · holobiomicslab

    Use when when you have identified the set of analytes (peptides, nucleosides, or other biomolecules) you wish to simulate in silico, and you need to prepare their chemical properties (m/z, intensity, retention time) in a machine-readable format before applying fragmentation and noise injection.
    1 install
46. ▌
    Peptide Isotopic Envelope Calculation · holobiomicslab

    Use when you have a peptide sequence, precursor charge state, and observed m/z spectrum and need to generate the expected isotopic distribution to match against observed precursor or fragment ion peaks. This is especially critical in SIP workflows where incorporation probabilities (e.g., 0.
    2 installs
47. ▌
    Precursor Ion Chromatogram Extraction · holobiomicslab

    Use when you have raw DIA mass spectrometry data files (.raw, .d, or .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to extract precursor ion chromatograms for quality assessment or downstream analysis.
    2 installs
48. ▌
    Precursor Mass Difference Calculation · holobiomicslab

    Use when when comparing two MS/MS spectra using modified cosine similarity and the precursor m/z values differ, indicating potential neutral losses, adduct variations, or analogs with different substituents.
    0 installs
49. ▌
    Precursor Peak Removal Mass Tolerance · holobiomicslab

    Use when after loading an MsmsSpectrum object but before intensity filtering or spectral annotation.
    0 installs
50. ▌
    R Bioconductor Workflow Orchestration · holobiomicslab

    Use when you have untargeted LC/MS metabolomics data from stable isotope labeling experiments (e.g., 13C-glucose vs. 12C-glucose) already converted to mzXML format, and you need to systematically identify putatively incorporated metabolic features by comparing unlabeled and labeled sample groups.
    2 installs
51. ▌
    R Python Interoperability Via Wrapper · holobiomicslab

    Use when you have a Spectra object in R and need to apply a specialized Python MS algorithm (e.
    2 installs
52. ▌
    Rc Object Construction And Validation · holobiomicslab

    Use when after feature detection and alignment (XCMS or equivalent), when you have a CSV feature table with m/z and retention time columns and need to group features derived from the same compound.
    2 installs
53. ▌
    Reaction Propensity Score Computation · holobiomicslab

    Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with reaction-metabolite associations) to estimate how differences in substrate availability—independent of gene expression—translate into.
    0 installs
54. ▌
    Redundant Feature Identification Lcms · holobiomicslab

    Use when after alignment of two or more same-method nontargeted LCMS datasets (e.g., via Eclipse) when you have a feature table containing retention times and feature intensities across samples. Use it when redundancy is expected—e.
    0 installs
55. ▌
    Relative Mass Defect Window Filtering · holobiomicslab

    Use when apply this filter when working with MS-DIAL peak lists (feature tables with m/z, retention time, and intensity) that contain features with anomalous mass defects—particularly when you have prior knowledge of the expected RMD range for your sample type or analytical method, or when you want.
    0 installs
56. ▌
    Retention Time And Mz Based Alignment · holobiomicslab

    Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each sample.
    2 installs
57. ▌
    Retention Time Mapping Spline Fitting · holobiomicslab

    Use when after anchor feature pairs (m/z and retention time values) have been selected from two disparately-acquired LC-MS datasets, and you need to correct for systematic retention time differences between the datasets.
    0 installs
58. ▌
    Routing Module Testing And Validation · holobiomicslab

    Use when when you have implemented conditional routing logic in the GNPS_MASST codebase and need to verify that spectrum submissions with explicit domain-context selections (e.
    0 installs
59. ▌
    Scan Window Routing Mass Spectrometry · holobiomicslab

    Use when when processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution.
    2 installs
60. ▌
    Scoring Function Sensitivity Analysis · holobiomicslab

    Use when you have two or more complementary scoring functions (e.g., strain correlation and IOKR scores) that you wish to combine, and you need to determine which combination strategy and parameters maximize enrichment of known true links in a validation set.
    0 installs
61. ▌
    Shell Scripting For Program Discovery · holobiomicslab

    Use when a scientific application (such as QCxMS2) requires multiple external programs with specific version constraints and you need to programmatically verify their presence and compatibility before executing calculations.
    0 installs
62. ▌
    Sinusoidal Positional Encoding Design · holobiomicslab

    Use when you have variable-length lists of MS/MS peaks (m/z and intensity pairs) that need to be encoded into a fixed-dimensional representation compatible with transformer architecture.
    0 installs
63. ▌
    Sparse Distance Matrix Interpretation · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes (containing only cosine distances between neighboring spectra, not exhaustive pairwise comparisons) and need to partition spectra into groups of similar ions or peptides.
    0 installs
64. ▌
    Spectral Data Loading From Repository · holobiomicslab

    Use when when you need to retrieve a specific MS/MS spectrum from a public proteomics repository (PRIDE, MassIVE, PeptideAtlas) by its USI string for annotation, visualization, or comparative analysis, rather than working with locally stored mzML/mzXML files or already-loaded spectrum objects.
    0 installs
65. ▌
    Spectral Fragmentation Motif Analysis · holobiomicslab

    Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score these groups by their differential activity across experimental conditions, especially when traditional pathway databases.
    1 install
66. ▌
    Spectral Library Integration Workflow · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS data targeting lipid species not adequately covered by LipidMatch's built-in library (500,000+ species across 60+ lipid types), or when working with specialized applications requiring custom lipid definitions (e.
    2 installs
67. ▌
    Spectral Library Match Classification · holobiomicslab

    Use when when you have run MS2Query on query MS/MS spectra and obtained results with library matches that need to be disambiguated into two categories: (1) exact matches (precursor m/z difference near zero) versus (2) analog matches (chemically related but different precursor m/z).
    0 installs
68. ▌
    Spectral Network Propagation Analysis · holobiomicslab

    Use when after running MetaMiner's Dereplicator stage to identify some RiPPs via direct database matching against a constructed structure database, apply this skill to enlarge the set of identifications by propagating those matches through spectral clusters and visualizing the connected components.
    2 installs
69. ▌
    Spectral Peak Detection Composite Map · holobiomicslab

    Use when when you have aligned mass tracks (extracted ion chromatograms) across multiple LC-MS samples consolidated into a composite map and need to detect reproducible elution peaks (features) that will be tracked back to individual samples.
    2 installs
70. ▌
    Spectral Peak Grouping Mass Tolerance · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument measurement uncertainty.
    0 installs
71. ▌
    Spectral Peak Intensity Normalization · holobiomicslab

    Use when after loading raw m/z peak data (in MetaboAnalyst, MetaboShiny native, or Metabolights format) and merging it with sample metadata (batch IDs, concentration values, experimental group labels).
    0 installs
72. ▌
    Spectral Peak Matching With Tolerance · holobiomicslab

    Use when when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks. Use this skill before calculating similarity scores (cosine, entropy, Bhattacharyya) or when applying penalty factors to unmatched peaks.
    0 installs
73. ▌
    Spectral Quality Assurance Proteomics · holobiomicslab

    Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment ions rise substantially above noise—i.
    0 installs
74. ▌
    Spectral Similarity Score Computation · holobiomicslab

    Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a continuous scale (Tanimoto prediction).
    0 installs
75. ▌
    Standalone Web Application Deployment · holobiomicslab

    Use when you have cloned the GNPS_MASST codebase and need to instantiate a domain-specific MASST variant (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) to accept individual MS/MS spectra as input queries and perform searches against the corresponding curated reference.
    0 installs
76. ▌
    Statistical Visualization Multi Group · holobiomicslab

    Use when when you have loaded search results from two or more DIA-MS analysis tools (e.
    0 installs
77. ▌
    Subformula Assignment Neural Networks · holobiomicslab

    Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational overhead of generating full SIRIUS fragmentation trees or do not have access to spectrum databases.
    2 installs
78. ▌
    Substrate Concentration Normalization · holobiomicslab

    Use when you have LC-MS normalized intracellular metabolite abundance data from multiple cell lines (or samples) and need to compute reaction-level propensity scores that account for substrate availability as a predictor of metabolic flux.
    0 installs
79. ▌
    Tanimoto Score Threshold Optimization · holobiomicslab

    Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision threshold for classifying spectrum pairs as 'chemically related' or 'unrelated'.
    0 installs
80. ▌
    Targeted Feature Extraction From Lcms · holobiomicslab

    Use when you have a curated target list of m/z values, retention times, and identifiers for specific metabolites of interest, and you want to extract only those features from LC-MS data (mzML or netCDF format) rather than performing untargeted feature discovery.
    0 installs
81. ▌
    Targeted Proteomics Feature Filtering · holobiomicslab

    Use when you have loaded transition group chromatogram data from sqMass files and need to restrict the analyte selection dropdowns (protein, peptide, charge state) to only those features passing a specified Q-value threshold (default 1%), or when you need to selectively display or hide MS1 and MS2.
    0 installs
82. ▌
    Tensor Operation Element Wise Product · holobiomicslab

    Use when you have two embedding tensors of identical shape (e.g., both 512-dimensional) and need to produce a fused representation that captures multiplicative interactions between modalities.
    0 installs
83. ▌
    Threshold Based Sample Classification · holobiomicslab

    Use when after normalization (step 7) in untargeted metabolomic profiling pipelines, when you have a preprocessed feature matrix and need to identify samples with anomalous metabolic profiles that violate multivariate assumptions or represent technical failures.
    2 installs
84. ▌
    Ms1 Feature Peak Detection In Full Scan · holobiomicslab

    Use when you have merged MS1 spectra (output from spectral binning/merging steps) from a full-scan FIA-MS or LC-MS acquisition and need to identify distinct molecular features before accurate mass annotation or background filtering.
    0 installs
85. ▌
    Natural Product Classifier Substitution · holobiomicslab

    Use when gNPS has ceased supplying ClassyFire ontology information for spectral library matches, causing downstream ConCISE consensus classification to fail or produce incomplete ontology fields.
    0 installs
86. ▌
    Natural Products Workflow Orchestration · holobiomicslab

    Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to generate a Wikidata-connected RDF knowledge graph for integrated natural products analysis, taxonomy-aware compound.
    0 installs
87. ▌
    Network Based Metabolite Identification · holobiomicslab

    Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
    0 installs
88. ▌
    Network Graph Re Annotation Propagation · holobiomicslab

    Use when when you have completed an initial ModiFinder analysis on a compound pair (known compound + modified analog with unknown structure), and you subsequently acquire or determine the structure of the modified compound.
    0 installs
89. ▌
    Nontargeted Analysis Workflow Execution · holobiomicslab

    Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for MSThunder input, and you need to identify unknown organic pollutants with deep learning-assisted structure prediction and.
    2 installs
90. ▌
    Numpress Compression Algorithm Encoding · holobiomicslab

    Use when you have raw floating-point m/z and intensity arrays extracted from mass-spectrometry experiments (e.g., from mzML or mzXML files) and need to compress them for storage or transmission.
    2 installs
91. ▌
    Parental Signal Selection From Clusters · holobiomicslab

    Use when after feature clustering has grouped LC-MS peaks by MS-DIAL peak character estimation, you need to reduce the cluster to a single representative feature per biological entity.
    0 installs
92. ▌
    Peak Boundary Definition And Validation · holobiomicslab

    Use when after nontargeted peak detection has identified candidate peaks in LC-MS chromatograms, when you need to establish exact peak start/end retention times and extract peak-level metadata (intensity, width, shape) for downstream feature quality evaluation and annotation workflows.
    0 installs
93. ▌
    Peak Intensity Removal And Thresholding · holobiomicslab

    Use when when you have imported raw mass spectrometry spectral data (in formats like mzML, mzXML, msp, MGF, or JSON) and need to clean peak lists before metadata validation, similarity scoring, or library comparison.
    0 installs
94. ▌
    Peak To Metabolite Candidate Assignment · holobiomicslab

    Use when you have a raw peak-intensity matrix from untargeted LC-MS data (organized as rows=peaks, columns=samples) and need to generate initial candidate metabolite assignments.
    0 installs
95. ▌
    Peptide B Y Ion Theoretical Calculation · holobiomicslab

    Use when when you have a peptide sequence and need to predict which fragment ions (B and Y series) should appear in an MS2 spectrum at a known isotopic abundance (e.g., natural 13C at 1.07%, or stable isotope labeling at 50% enrichment).
    0 installs
96. ▌
    Peptide Sequence To Spectrum Conversion · holobiomicslab

    Use when when you have a peptide sequence and need to predict its fragmentation pattern under specific isotopic labeling conditions (e.g., natural 13C abundance at 1%, or enriched 13C at arbitrary levels).
    1 install
97. ▌
    Per Sample Feature Composition Analysis · holobiomicslab

    Use when when you have aligned and quantified mass spectrometry features from multiple natural extracts (via MZmine2/3), paired with in silico annotation results (ISDB or SIRIUS), and you need to prioritize samples for chemical discovery based on the proportion of unannotated, extract-specific.
    0 installs
98. ▌
    Podp Metadata Retrieval And Integration · holobiomicslab

    Use when when running NPLinker in PODP mode (as opposed to local mode), you need to fetch and validate project metadata from PODP, orchestrate downloads of GNPS molecular networking data, AntiSMASH BGC predictions, BigScape clustering results, and MIBiG reference metadata, then organize them into.
    0 installs
99. ▌
    Precursor Mass Neutral Loss Calculation · holobiomicslab

    Use when when analyzing tandem mass spectra (MS/MS data) and you want to incorporate neutral loss patterns—characteristic mass losses from molecular precursors—into your spectral similarity or feature representation.
    0 installs
100. ▌
     Pytorch Model Training And Optimization · holobiomicslab

     Use when when you have preprocessed molecular graph representations (from Preprocess.py or equivalent) and need to train a regression model to predict continuous retention time targets.
     0 installs