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HolobiomicsLab

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1. ▌
   Gzip Index Structure Parsing 2 · holobiomicslab

   Use when when you have an indexed gzip-compressed mzML file (mzML.gz with an internal index) and need to retrieve specific spectra or chromatogram data blocks by integer index without decompressing the entire archive.
   5 installs
2. ▌
   Qc Summary Table Extraction 3 · holobiomicslab

   Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain a structured report of which ions passed or failed each filter.
   7 installs
3. ▌
   R6 Object Method Invocation 3 · holobiomicslab

   Use when when working with large metabolomics peak tables (e.
   7 installs
4. ▌
   Repository Code Integration 3 · holobiomicslab

   Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public repository, and you need to apply that method to new experimental data (e.
   7 installs
5. ▌
   Scoring Module Unit Testing 3 · holobiomicslab

   Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring logic into an existing MS2Query pipeline.
   5 installs
6. ▌
   Spec2vec Similarity Scoring 3 · holobiomicslab

   Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation pattern against a pre-indexed spectral library using learned spectral embeddings.
   5 installs
7. ▌
   Spectral Mz Range Filtering 3 · holobiomicslab

   Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment (e.g., 100–1400 m/z for typical tryptic peptides).
   5 installs
8. ▌
   Spectral Similarity Ranking 3 · holobiomicslab

   Use when you have a query MS/MS spectrum and need to identify the -matching library spectrum from a large spectral database, particularly when the research goal requires distinguishing between exact matches and structural analogues without separate workflows.
   5 installs
9. ▌
   Spectrum Cluster Assignment 3 · holobiomicslab

   Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters. Use this skill when: (1) you have a sparse similarity or distance matrix as input;
   3 installs
10. ▌
    Unique Compound Enumeration 3 · holobiomicslab

    Use when you have a GC-MS results table with a Match.Factor column (representing identification confidence) and you need to understand how many distinct compounds survive at different quality cutoffs (e.g., ≥65, ≥80, ≥90).
    3 installs
11. ▌
    Web Service API Integration 3 · holobiomicslab

    Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular fingerprint predictions, de-novo candidate structures, or chemical class annotations without maintaining local neural network.
    5 installs
12. ▌
    Twim Ms Data Processing 3 · holobiomicslab

    Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign unidentified features to biomolecular classes (e.
    5 installs
13. ▌
    Arrow Table Serialization 3 · holobiomicslab

    Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist them to disk in Parquet format for downstream analysis, interoperability with other languages (R, .
    6 installs
14. ▌
    CI CD Workflow Monitoring 3 · holobiomicslab

    Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts, or fails in a reproducible manner.
    4 installs
15. ▌
    Mzpeak File Io Operations 3 · holobiomicslab

    Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability across languages and tools; (2) load mzPeak spectrum or chromatogram data into memory as structured tables for analysis;
    7 installs
16. ▌
    Pathway Database Querying 3 · holobiomicslab

    Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full pathway database should serve as the statistical background, and which pathways contain how many metabolites overall.
    4 installs
17. ▌
    Spectrum Array Validation 3 · holobiomicslab

    Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to confirm that the resulting arrays fall within specified m/z windows, intensity bounds, and peak count limits before.
    5 installs
18. ▌
    Feature Group Spectral Mapping 2 · holobiomicslab

    Use when after sample alignment and isotopologue/adduct grouping are complete, when you need to associate MS2 spectral data (DDA-acquired) with the consolidated feature groups to enable MS/MS-based compound annotation or to bundle MS1 quantification with MS2 evidence.
    5 installs
19. ▌
    Gaussian Peak Shape Evaluation 4 · holobiomicslab

    Use when after peak detection on a composite mass track has identified candidate peaks in a mass chromatogram, and before compiling the final feature table.
    5 installs
20. ▌
    Metabolomics Sample Comparison 2 · holobiomicslab

    Use when you have a MemoMatrix (sample-by-fingerprint matrix) from aligned MS2 spectra and need to visually compare sample similarity or clustering patterns, especially when samples show poor feature overlap, strong retention time shifts across different LC methods, or were acquired on different.
    4 installs
21. ▌
    Annotation Object Manipulation 3 · holobiomicslab

    Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate annotations per feature, visualize matched ions in ranked spectra, or export pseudo-MS/MS spectra for external analysis.
    5 installs
22. ▌
    Compressed File Header Parsing 2 · holobiomicslab

    Use when you have a large indexed gzip file (igz format) with metadata encoded in the gzip header comment field, and you need to retrieve specific blocks or spectra by integer index without decompressing the entire file.
    7 installs
23. ▌
    Control Flow Diagram Synthesis 4 · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on declared input type (LC, GC, IMS, or MS Imaging).
    6 installs
24. ▌
    Dimensionality Reduction T Sne 3 · holobiomicslab

    Use when you have computed high-dimensional embeddings (e.
    5 installs
25. ▌
    Feature List Format Validation 3 · holobiomicslab

    Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic detection, or wishes to augment/replace pyOpenMS results with pre-processed features.
    6 installs
26. ▌
    Fragment Ion Database Matching 3 · holobiomicslab

    Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment libraries (e.g., LipidPos for lipids).
    5 installs
27. ▌
    Ggplot2 Geom Treemap Rendering 3 · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).
    6 installs
28. ▌
    High Dimensional Data Indexing 3 · holobiomicslab

    Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest neighbors efficiently.
    7 installs
29. ▌
    Inter Scan Interval Validation 3 · holobiomicslab

    Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the scheduled method with correct temporal spacing.
    5 installs
30. ▌
    Iokr Fingerprint Space Ranking 3 · holobiomicslab

    Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a compound-class-agnostic method.
    6 installs
31. ▌
    Lc Ms Adduct Pattern Detection 3 · holobiomicslab

    Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may represent the same compound ionized as different adducts (e.g., [M+H]⁺ vs. [M+Na]⁺).
    5 installs
32. ▌
    Lda Model Training Convergence 3 · holobiomicslab

    Use when you have a preprocessed bag-of-fragments corpus derived from tandem mass spectrometry spectra and need to discover recurring fragmentation motifs without prior compound identification.
    4 installs
33. ▌
    Ms Dial Export Format Handling 3 · holobiomicslab

    Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool. The skill is required whenever you are preparing MS-DIAL output for consumption by external analysis pipelines that expect standardized export formats.
    5 installs
34. ▌
    Multi Cell Line Rps Calculation 2 · holobiomicslab

    Use when when you have LC-MS normalized intracellular metabolite abundance measurements for multiple cell lines and need to estimate reaction activity driven by substrate availability rather than enzyme expression alone.
    5 installs
35. ▌
    Nearest Neighbor Index Querying 3 · holobiomicslab

    Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by precursor m/z).
    6 installs
36. ▌
    Neural Network Model Deployment 3 · holobiomicslab

    Use when you have LC-MS feature tables (m/z and retention time columns) and corresponding .mzXML or .mzML files, and you need to automatically classify whether extracted ion chromatograms represent genuine metabolomic features or false positives.
    5 installs
37. ▌
    Object State Mutation Detection 3 · holobiomicslab

    Use when when calling filter functions (e.g., filter_mispicked_ions(), filter_group(), filter_cv()) on R6-based metabolomics data objects in the mpactr package and you need to verify whether the original object's state is preserved.
    5 installs
38. ▌
    Peak Detection Cwt Optimization 3 · holobiomicslab

    Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.
    5 installs
39. ▌
    Peak Table Row Count Comparison 2 · holobiomicslab

    Use when you need to validate the reference-semantics behavior of mpactr filter functions, particularly when using copy_object=FALSE. Use it to confirm that a filtering operation (e.
    7 installs
40. ▌
    Peakmap Heatmap Rendering Mz Rt 3 · holobiomicslab

    Use when when you have mass spectrometry data organized in a Pandas DataFrame with m/z values, retention time (RT), and intensity measurements, and you want to visualize the joint distribution and correlation of these three dimensions to identify peaks, assess separation, and detect patterns across.
    7 installs
41. ▌
    Peptide Level Spectrum Grouping 2 · holobiomicslab

    Use when after embedding MS/MS spectra into a 32-dimensional vector space using GLEAMS, when you need to identify and group all spectra originating from the same peptide sequence.
    8 installs
42. ▌
    Ppm Tolerance Window Adjustment 2 · holobiomicslab

    Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.
    5 installs
43. ▌
    Python Automated Test Execution 2 · holobiomicslab

    Use when when contributing code changes to a Python project (fork, feature branch, or pull request) that uses a setup.py-based test suite, before pushing changes to the remote repository or merging into the main branch.
    6 installs
44. ▌
    Pytorch Tensor Shape Validation 2 · holobiomicslab

    Use when after implementing a transformer encoder backbone with masking mechanisms in PyTorch, before training on mass spectra data.
    5 installs
45. ▌
    Raw Chromatography Data Parsing 4 · holobiomicslab

    Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral analysis.
    8 installs
46. ▌
    Restful API Endpoint Invocation 3 · holobiomicslab

    Use when you have NMR peak data (1H and 13C chemical shift values) and need to obtain SMART 3 classification predictions from the DeepSAT service.
    7 installs
47. ▌
    Retention Order Prediction Rplc 2 · holobiomicslab

    Use when when you have a set of small molecules (as SMILES or structures) that need to be identified or ranked by their elution order in RPLC systems with acidic pH (~2.7), and you want to assess model confidence in retention predictions.
    5 installs
48. ▌
    Sample Partitioning By Metadata 2 · holobiomicslab

    Use when you have a merged MGF file (e.g., from MZmine output) containing MS/MS spectra from multiple biological or environmental samples, and you need to process each sample independently through annotation pipelines (e.
    6 installs
49. ▌
    CI CD Workflow Triggering 3 · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that automated build infrastructure is functioning correctly.
    5 installs
50. ▌
    Release Branch Management 3 · holobiomicslab

    Use when you need to validate that a software project's release branch is stable and ready for distribution. Specifically, use it when: (1) a release tag has been created or code pushed to a release branch; (2) you need to confirm that CI/CD pipelines execute without failures;
    5 installs
51. ▌
    Repository Administration 3 · holobiomicslab

    Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing new versions, after merging changes to release branches, or when troubleshooting build failures that block distribution of.
    6 installs
52. ▌
    CI CD Pipeline Orchestration 3 · holobiomicslab

    Use when you need to automate testing and quality checks on code changes—specifically when pull requests or commits are made to a repository and you want to verify that builds succeed, test suites pass, and code quality metrics meet project standards before merging.
    7 installs
53. ▌
    Feature Annotation Filtering 3 · holobiomicslab

    Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among thousands of detected features.
    8 installs
54. ▌
    Filter Output Interpretation 3 · holobiomicslab

    Use when after applying a filter function (filter_mispicked_ions(), filter_group(), filter_cv(), filter_insource_ions()) to an mpactr object, use this skill to inspect and document which features were retained versus removed.
    6 installs
55. ▌
    Fragmentation Motif Learning 3 · holobiomicslab

    Use when you have preprocessed mass spectrometry fragmentation data (neutral losses and fragment masses extracted and noise-filtered) and want to discover hidden structural motifs across a spectral dataset in an unsupervised manner.
    5 installs
56. ▌
    Gc Ms Spectral Deconvolution 4 · holobiomicslab

    Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be resolved by simple peak picking.
    4 installs
57. ▌
    Installation Troubleshooting 3 · holobiomicslab

    Use when when setting up matchms for the first time in a new environment, after upgrading Python or conda, when switching between package managers (pip vs conda), or when distributing matchms to end users to confirm functionality across supported installation channels.
    5 installs
58. ▌
    Instrumental Drift Detection 3 · holobiomicslab

    Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex Multiquant software (v3.0.
    6 installs
59. ▌
    Ms Ms Spectrum Peak Annotation 3 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or local data) and need to identify significant fragment ions above noise, assign occurrence scores to peaks, and generate a CSV-formatted library entry for use in metabolite feature annotation pipelines.
    8 installs
60. ▌
    Ms2 Fingerprint Matrix Merging 3 · holobiomicslab

    Use when you have two MemoMatrix objects generated from separate sample cohorts (e.
    5 installs
61. ▌
    Multi Panel Spectra Comparison 3 · holobiomicslab

    Use when when you need to visually compare two or more spectra (MS1, MS2, or extracted ion chromatograms) across different retention times, m/z ranges, or ion mobility bins in a single figure. Apply this skill after extracting spectra arrays from MZA files (e.
    5 installs
62. ▌
    Nmr Modality Ablation Analysis 3 · holobiomicslab

    Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal contribution of each NMR modality or justify multimodal input design.
    7 installs
63. ▌
    Peak Classification Validation 3 · holobiomicslab

    Use when after training or loading a NeatMS neural network model, before applying it to filter false positive MS1 peaks in a new dataset.
    6 installs
64. ▌
    Precursor Product Mass Pairing 3 · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment masses.
    6 installs
65. ▌
    Ranking Performance Evaluation 2 · holobiomicslab

    Use when after running retention-order prediction experiments on a test or held-out evaluation dataset.
    8 installs
66. ▌
    Retention Time Drift Detection 2 · holobiomicslab

    Use when you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect misalignment of feature groups.
    6 installs
67. ▌
    Signal Intensity Normalization 2 · holobiomicslab

    Use when after loading raw LC-MS data from multiple disease groups when you need to compute correlations between metabolite signals and disease classes, or before training a deep learning model on metabolomics profiles.
    6 installs
68. ▌
    Simulation Parameter Variation 2 · holobiomicslab

    Use when when you have a computational simulation framework (e.
    5 installs
69. ▌
    Spectral Corpus Representation 3 · holobiomicslab

    Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
    5 installs
70. ▌
    Spectral Feature Consolidation 3 · holobiomicslab

    Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint data into a single matrix for comparative analysis.
    8 installs
71. ▌
    Spectral Feature Normalization 2 · holobiomicslab

    Use when when you have raw LC-MS metabolomics data in .mzML or .npy format from multiple disease groups with varying ionization efficiencies or detector sensitivities, and you need to train a deep learning model for disease classification.
    5 installs
72. ▌
    Spectral Library Matching Ripp 3 · holobiomicslab

    Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by matching experimental spectra against a database of predicted post-translationally modified RiPP structures derived from.
    6 installs
73. ▌
    Spectral Peak Network Grouping 2 · holobiomicslab

    Use when after peak picking has been completed on INADEQUATE NMR spectra and you need to group correlated peaks into compound-specific networks before matching against a metabolite database.
    5 installs
74. ▌
    Substructural Motif Annotation 3 · holobiomicslab

    Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to associate each network node with its constituent substructural motifs and visualize which motifs are shared between.
    6 installs
75. ▌
    Scikit Learn Metric Computation 2 · holobiomicslab

    Use when you have prediction arrays (model outputs) and ground-truth label arrays from a classification task and need to compute confusion matrices, accuracy scores, or other performance metrics for visualization or quantitative evaluation.
    7 installs
76. ▌
    Simulation Output Serialization 2 · holobiomicslab

    Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans, and fragmentation events in memory.
    5 installs
77. ▌
    Spectral Alignment Optimization 2 · holobiomicslab

    Use when when you have two MS/MS fragmentation spectra (with precursor m/z values and fragment ion lists) and need to establish correspondence between their fragment ions beyond simple pairwise comparison.
    5 installs
78. ▌
    Spectral Connectivity Filtering 2 · holobiomicslab

    Use when you have picked peaks (coordinates and intensities) from an INADEQUATE NMR spectrum and need to cluster them into networks representing individual compounds.
    4 installs
79. ▌
    Spectral Data Quality Assurance 2 · holobiomicslab

    Use when when importing raw mass spectrometry data in formats like mzML, mzXML, msp, MGF, or JSON and you need to ensure spectral data quality before proceeding to similarity comparisons or other downstream analyses.
    5 installs
80. ▌
    Spectral File Format Conversion 3 · holobiomicslab

    Use when when you have a GNPS molecular networking job archive (downloaded as a .zip or compressed archive) and need to prepare metabolomics spectra and molecular family data for NPLinker integration.
    4 installs
81. ▌
    Spectral Precursor Peak Removal 2 · holobiomicslab

    Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry experiment (e.g., via USI) and before intensity filtering or scaling.
    6 installs
82. ▌
    Spectral Similarity Computation 3 · holobiomicslab

    Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
    5 installs
83. ▌
    Spectrum Subsetting And Merging 2 · holobiomicslab

    Use when when you have a large MsBackend object and need to (1) select a contiguous or non-contiguous range of spectra for focused analysis, or (2) combine spectra from multiple independently-loaded backends (e.
    5 installs
84. ▌
    Strain Spectrum Mapping Linkage 2 · holobiomicslab

    Use when when you have downloaded and extracted a GNPS archive (from GNPS1 or GNPS2 workflows) and need to establish which spectral records (from spectra.mgf) were generated from which bacterial strains or samples. The file_mappings.tsv or file_mappings.
    4 installs
85. ▌
    Swath Ms Spectrum Deconvolution 2 · holobiomicslab

    Use when you have SWATH-MS raw data (mzML or vendor format) from an untargeted metabolomics experiment and need to identify metabolites.
    4 installs
86. ▌
    Tandem Mass Spectrum Clustering 3 · holobiomicslab

    Use when you have a large collection of tandem mass spectra (mzML, mzXML, or MGF format) and want to group similar spectra into clusters to identify redundancy, discover novel peptides or metabolites, or prepare data for downstream annotation.
    5 installs
87. ▌
    Validation Error Categorization 2 · holobiomicslab

    Use when when a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification. Apply this skill after loading the mwTab file using the mwtab parser but before quality assurance sign-off or deposition to the Metabolomics Workbench.
    5 installs
88. ▌
    Lipid Candidate Matching 3 · holobiomicslab

    Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
    5 installs
89. ▌
    Mzml Mzxml Spectrum Reading 2 · holobiomicslab

    Use when when you have raw mzML or mzXML files containing uncompressed m/z and intensity arrays and need to load spectra into a uniform data contract before compression, cross-format comparison, or algorithmic processing.
    5 installs
90. ▌
    Reference Library Alignment 3 · holobiomicslab

    Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or enable CCS correction by comparing measured lipids against known library entries with validated CCS values.
    3 installs
91. ▌
    Twim Ms Calibration Mapping 3 · holobiomicslab

    Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.
    6 installs
92. ▌
    Gcf Spectra Association Ranking 2 · holobiomicslab

    Use when when you have integrated genomic data (GCFs from AntiSMASH via BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to identify and rank which secondary metabolites detected in spectra are likely produced by which biosynthetic.
    7 installs
93. ▌
    Gnps Workflow Result Processing 3 · holobiomicslab

    Use when when you have run a spectral networking job on GNPS (e.g. ProteoSAFe-METABOLOMICS-SNETS-V2) and need to reuse the network output files locally with MetaMiner or another tool that accepts spectral network input directories.
    5 installs
94. ▌
    Inchikey Smiles Standardization 2 · holobiomicslab

    Use when when you have raw MS/MS spectra from repositories like GNPS that lack or have inconsistent chemical structure annotations (InChI/SMILES), and you need to produce a curated dataset with uniform 14-character InChIKey and SMILES/InChI annotations for downstream machine learning or similarity.
    5 installs
95. ▌
    Kegg Identifier To Mass Mapping 2 · holobiomicslab

    Use when you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites. This skill must be applied before the matching stage if you are working with a KEGG database (KeggDB or sample.keggDB) and require a precomputed adduct/fragment lookup table.
    4 installs
96. ▌
    Lc Ms Retention Time Adjustment 2 · holobiomicslab

    Use when you have centroided .mzML LC–MS data with multiple sample runs and a preliminary compound target table with theoretical or measured retention times, but you suspect the expected RT values may not align with actual retention windows in your dataset.
    5 installs
97. ▌
    Mass Spectral Data Augmentation 2 · holobiomicslab

    Use when when you have limited real GC-MS overlapped peak data but need thousands of labeled examples to train a deep learning model for mass spectral deconvolution.
    4 installs
98. ▌
    Mass Spectrometry Scan Indexing 2 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs. MSn to enable level-specific filtering, (3) retrieve scan ranges or specific scan numbers for targeted spectral extraction, or (4) plan.
    4 installs
99. ▌
    Mass Spectrum Adduct Assignment 2 · holobiomicslab

    Use when when analyzing tandem mass spectra with unknown precursor adduct identity, especially for positive-mode data containing non-protonated adducts ([M+Na]+, [M+K]+, [M+NH4]+).
    6 installs
100. ▌
     Metabolite Cv Ratio Calculation 2 · holobiomicslab

     Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment. Use it to remove features that are poorly reproducible or show inconsistent signal across samples relative to instrument/technical variation.
     6 installs