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HolobiomicsLab

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1. ▌
   Gc Column Polarity Specific Ri Filtering · holobiomicslab

   Use when you have a combined EI mass spectral library (MSP format) lacking experimental RI values, access to NIST ri.dat and USER.
   2 installs
2. ▌
   Mass Spectrometry Data Format Conversion · holobiomicslab

   Use when you have mass spectral libraries from multiple sources (e.g., NIST EI, RIKEN MS2, MoNA GC-MS or LC-MS/MS, GNPS mgf) that need to be consolidated for use in MS-DIAL, or you have a single library with incomplete or malformed metadata (e.
   0 installs
3. ▌
   Mass Spectrometry Data Quality Filtering · holobiomicslab

   Use when you have generated a complete feature table from mzML files (e.g., Asari 'full' feature table) and need to curate it for downstream analysis.
   2 installs
4. ▌
   Mass Spectrometry Match Factor Filtering · holobiomicslab

   Use when you have a GC-MS dataset with a Match.Factor column (output from Agilent Unknowns Analysis or equivalent) and need to retain only high-confidence compound identifications.
   0 installs
5. ▌
   Metabolomic Feature Extraction From Mzml · holobiomicslab

   Use when you have centroid mzML files from LC-MS acquisitions and need to detect, group, and quantify metabolomic features for a PCPFM experiment. Use it as the first feature-level processing step after file format conversion from raw instrument files (e.g., .raw to mzML via ThermoRawFileParser).
   0 installs
6. ▌
   Overlapped Peak Deconvolution Validation · holobiomicslab

   Use when after solving for the concentration distribution matrix C using least squares optimization (minimize ||overlapped_peaks - S·C||²), validate that the solution is physically meaningful and numerically accurate by checking whether S·C faithfully reconstructs the input overlapped peak.
   0 installs
7. ▌
   Retention Index Assignment And Filtering · holobiomicslab

   Use when after combining multiple EI or MS2 mass spectral libraries and you have access to NIST RI reference files (ri.dat and USER.DBU) and need to assign experimental retention indices to compounds.
   0 installs
8. ▌
   Spectral Library Compilation And Merging · holobiomicslab

   Use when you have multiple mass spectral library files in different formats (MSP, MGF, MOL folders) from sources like NIST, MoNA, RIKEN, or GNPS, and need to produce a single consolidated MSP file with complete SMILES, InChIKey, and experimental retention index (RI) annotations for metabolomics or.
   2 installs
9. ▌
   Spectral Library Metadata Reorganization · holobiomicslab

   Use when when ingesting mass spectral libraries (EI or MS2) where SMILES information is embedded in the Comment field rather than in a dedicated SMILES metadata field—particularly common in MoNA GC-MS and LC-MS/MS exports.
   0 installs
10. ▌
    Ablation Study Design And Interpretation · holobiomicslab

    Use when when you have a neural network or machine learning model with multiple tunable hyperparameters (layer size, regularization strength, dropout) or design choices (e.
    0 installs
11. ▌
    Annotation Candidate Comparative Scoring · holobiomicslab

    Use when you have pseudo-MS/MS spectra from LC-MS all-ion fragmentation (AIF) data that have been matched against one or more ion fragment databases (e.g., LipidPos, MassBank), generating multiple candidate annotations per feature.
    0 installs
12. ▌
    Batch Corrected Feature Table Validation · holobiomicslab

    Use when after applying batch correction (e.g., ComBat, SVA) to a merged feature table from non-targeted LC-MS/MS metabolomics data and before proceeding to univariate or multivariate statistical analysis.
    0 installs
13. ▌
    Bgc Identification From Genomic Sequence · holobiomicslab

    Use when you have assembled genome sequences (contigs or scaffolds in FASTA format) and want to identify putative BGCs and their precursor peptides before constructing a RiPP structure database for spectral matching.
    0 installs
14. ▌
    Bioconductor Backend Architecture Design · holobiomicslab

    Use when you are building a new mass spectrometry data backend or storage layer and need to integrate it with the Spectra ecosystem. Triggers include: (1) you have a novel data source (raw files, databases, web APIs) that should be accessible through Spectra objects;
    0 installs
15. ▌
    Bioconductor Object Structure Inspection · holobiomicslab

    Use when after constructing a SummarizedExperiment object from raw metabolomics data via buildExperiment, or after batch correction and ratio computation steps, inspect rowData, colData, and assays slots to verify that compound identities, sample annotations, and computed assay values (primary.
    2 installs
16. ▌
    Blind Search Mode Parameter Optimization · holobiomicslab

    Use when when you have tandem mass spectra from ribosomally synthesized peptides (RiPPs) and suspect the presence of unknown or non-standard post-translational modifications that would be missed by standard database search modes constrained to known modification classes.
    0 installs
17. ▌
    Chemical Noise Subformula Loss Filtering · holobiomicslab

    Use when you have MS/MS spectra with high chemical noise (spurious ions arising from incomplete ionization, in-source fragmentation, or instrument artifacts) and you possess accurate molecular formula or SMILES structure and adduct information for the precursor.
    2 installs
18. ▌
    Chromatographic Method Transfer Learning · holobiomicslab

    Use when you have experimental RT measurements from a source chromatographic method and need to predict RTs for the same molecules on a target chromatographic method, but lack a large calibration dataset (typical scenario: 10–100 molecules with ground truth RTs on both methods).
    2 installs
19. ▌
    Collision Cross Section Model Validation · holobiomicslab

    Use when after applying deimos.calibration.tunemix() to positive-mode or negative-mode tune mix data with known CCS reference compounds (m/z range typically 118–1522), verify that the resulting calibration model achieves the expected r-squared coefficient.
    2 installs
20. ▌
    Combined Table Extraction And Inspection · holobiomicslab

    Use when after constructing a metabCombiner object by grouping features from two metabData objects by m/z, and before proceeding to anchor selection, RT mapping, or alignment scoring.
    1 install
21. ▌
    Compound Structural Similarity Retrieval · holobiomicslab

    Use when you have a collection of preprocessed MS/MS spectra with structural annotations (InChIKey, SMILES, or InChI) and need to identify pairs of compounds that are structurally related above a specified similarity threshold.
    0 installs
22. ▌
    Correlation Matrix Heatmap Visualization · holobiomicslab

    Use when after computing a correlation matrix (e.g., Pearson correlation across samples) on statistically significant LC-MS features, particularly when you need to inspect hierarchical dendrogram structure, validate cluster assignments from different flattening methods (constant-threshold vs..
    0 installs
23. ▌
    Cross Method Chromatographic Scalability · holobiomicslab

    Use when you have a pretrained RT-Transformer model checkpoint from a large, well-characterized chromatographic dataset (e.g., SMRT) and need to predict retention times for a different chromatographic method or instrument condition represented in a smaller, domain-specific dataset (e.g., PredRet).
    2 installs
24. ▌
    Database Schema Design For Spectral Data · holobiomicslab

    Use when you have MS/MS spectral library data currently stored in file-based formats (JSON, CSV, binary, MGF, MSP) and need to migrate to database-backed storage to support fast queries by metadata filters (precursor m/z, ion mode, retention time) and computed similarity scores against query.
    0 installs
25. ▌
    Double Bond Positional Isomer Generation · holobiomicslab

    Use when when constructing a comprehensive lipid spectral reference library that must disambiguate lipids differing only in carbon-carbon double-bond position (e.
    1 install
26. ▌
    Embedding Space Dimensionality Reduction · holobiomicslab

    Use when when you have a collection of MS/MS spectra (in mzML or MGF format) and need to group or retrieve spectra from the same peptide, or when you need to perform large-scale similarity comparisons across millions of spectra without working directly in the original high-dimensional peak space.
    2 installs
27. ▌
    Experimental Design Metadata Integration · holobiomicslab

    Use when when you have LC-MS raw data and need to process it through a feature detection and quantification pipeline in KNIME, but lack a structured mapping between sample identifiers, experimental conditions, and the raw LC-MS runs.
    2 installs
28. ▌
    Feature Hashing Dimensionality Reduction · holobiomicslab

    Use when you have high-resolution tandem mass spectra (mzML, mzXML, or MGF format) and need to cluster or index millions of spectra efficiently without exhaustive pairwise comparison.
    2 installs
29. ▌
    Feature Matrix Normalization And Scaling · holobiomicslab

    Use when you have a heterogeneous feature matrix combining molecular descriptors (from RDKit/mordred) and chromatographic metadata (column length, temperature, pH, flow rate, particle size) with different physical units, ranges, and scales.
    0 installs
30. ▌
    Feature Metadata Parsing And Integration · holobiomicslab

    Use when after completing sample alignment in JPA (Part 5) or when ingesting a peaklist or aligned feature matrix from prior peak-picking runs, parse feature metadata to enable EIC export or multi-sample feature annotation.
    0 installs
31. ▌
    Feature Table Annotation Standardization · holobiomicslab

    Use when after Blueshift or Gravity processing has produced a feature abundance table with annotations, but before final reporting or integration with sample/injection metadata.
    2 installs
32. ▌
    Formula Database Chemical Noise Sampling · holobiomicslab

    Use when when you need to generate synthetic MS/MS spectra with chemical noise for validating denoising performance, benchmarking library matching algorithms, or testing edge cases where clean reference spectra exist but must be augmented with realistic contaminants.
    0 installs
33. ▌
    Function Wrapping And Binding Mechanisms · holobiomicslab

    Use when when you have Spectra objects in R and need to apply Python MS library functionality (spectral similarity scoring, filtering, normalization) without leaving the R environment, or when you want to create custom hybrid workflows that leverage both R and Python MS packages within a single.
    2 installs
34. ▌
    Gnps Spectral Library Compound Retrieval · holobiomicslab

    Use when you have GNPS library accession IDs (e.g. CCMSLIB00011906190) for a reference compound and a chemically or biologically modified analog, and need to load their full MS/MS spectra and structural annotations to set up a modification-finding analysis.
    2 installs
35. ▌
    High Resolution Mass Spectrum Processing · holobiomicslab

    Use when when you have high-resolution tandem mass spectra from proteomics experiments and need to search against a spectral library for both unmodified peptides and those with unknown or variable post-translational modifications.
    0 installs
36. ▌
    High Throughput Spectral Data Processing · holobiomicslab

    Use when when you have MGF-formatted mass spectrometry peak files (typically from proteomics experiments) numbering in the millions of spectra that require grouping into similar MS/MS clusters, and runtime must be kept under 15 minutes rather than hours.
    0 installs
37. ▌
    Identifier Format Parsing And Validation · holobiomicslab

    Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or a Feature-Based Molecular Networking (FBMN) identifier—and you need to programmatically determine which format was.
    0 installs
38. ▌
    Inchikey Normalization And Deduplication · holobiomicslab

    Use when you have an annotated MS/MS spectral dataset with structure metadata (InChI or SMILES records) linked to InChIKey identifiers, and you observe that some InChIKeys are associated with multiple or variant InChI strings due to curation inconsistencies, stereoisomerism notation differences, or.
    0 installs
39. ▌
    Inference Model Cpu Thread Configuration · holobiomicslab

    Use when when running Mass2SMILES inference on a TensorFlow-CPU build (e.g., delser292/mass2smiles:final container) and you need to optimize inference speed by controlling CPU core allocation.
    0 installs
40. ▌
    Installation Verification And Validation · holobiomicslab

    Use when after cloning the ENPKG repository and installing dependencies using uv sync or conda, before executing the workflow on metabolomics datasets.
    0 installs
41. ▌
    Isotope Labelling Feature Interpretation · holobiomicslab

    Use when after basepeak_finder has identified base peaks from isotope-labelled feature clusters with fold-change and intensity thresholds met.
    2 installs
42. ▌
    Lc Ms Feature Grouping By Retention Time · holobiomicslab

    Use when immediately after chromatographic peak detection (findChromPeaks) when you have detected peaks across multiple samples and need to identify which peaks represent the same feature across the sample cohort.
    2 installs
43. ▌
    Lda Convergence Monitoring And Iteration · holobiomicslab

    Use when after configuring LDA hyperparameters (alpha, beta, number of topics, iteration budget) and loading a preprocessed bag-of-fragments corpus with neutral losses extracted and noise filtered, initiate LDA training and apply convergence monitoring to determine when topic-fragment probability.
    4 installs
44. ▌
    Library Spectrum Database Format Parsing · holobiomicslab

    Use when you have experimental MS/MS spectra (from mzML, mzXML, or raw instrument formats) and wish to match them against a reference spectral library provided in MSP or CSV format. The skill is required as the first step before similarity scoring and candidate ranking.
    0 installs
45. ▌
    Mass Difference Calculation And Matching · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA) MS2 spectra from LC- or GC-HRMS and need to annotate detected features with PFAS-specific diagnostic fragments. Use it after feature detection (e.
    0 installs
46. ▌
    Mass Spectrometry Data Import And Export · holobiomicslab

    Use when use this skill at the start of any mass spectrometry analysis pipeline when you have raw spectral data in mzML, mzXML, msp, MGF, JSON, or metabolomics-USI format and need to load it into a Python environment for preprocessing, cleaning, filtering, or similarity comparison.
    2 installs
47. ▌
    Mass Spectrometry Data Structure Mapping · holobiomicslab

    Use when after feature extraction and peak recognition have produced detected MS/MS spectra (precursor m/z, charge, retention time, and fragment ion peaks), and you need to export these spectra for external spectral database searching, cross-platform comparison, or archival in a format compatible.
    0 installs
48. ▌
    Mass Spectrometry Feature Representation · holobiomicslab

    Use when after LC-MS feature clustering based on MS-DIAL peak character estimation, when you have grouped features that share similar chromatographic or spectral properties and need to select a single representative feature per cluster to reduce false positives and redundant annotations before.
    0 installs
49. ▌
    Mass Spectrometry Fragmentation Modeling · holobiomicslab

    Use when you are generating synthetic LC-MS/MS data for method validation, algorithm benchmarking, or co-fragmentation analysis, and need to model how specific biomolecules (peptides, nucleosides, or other chemical formulas) fragment under collision-induced dissociation.
    1 install
50. ▌
    Mass Spectrometry Qc Criteria Definition · holobiomicslab

    Use when when setting up a new LC-MS QC workflow or modifying existing QC rules: you have access to internal standards and target analytes, know their expected retention times and m/z values, and need to establish pass/fail boundaries for sample acceptance before or concurrent with instrument runs.
    0 installs
51. ▌
    Mass Spectrometry Raw Data Preprocessing · holobiomicslab

    Use when when you have raw DIA mass spectrometry data files (.raw, .d, .
    0 installs
52. ▌
    Mass Spectrometry Spectrum Vectorization · holobiomicslab

    Use when you have high-resolution MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search across millions of spectra. The vectorization step is necessary before constructing nearest-neighbor indexes or computing pairwise distance matrices for spectrum clustering.
    0 installs
53. ▌
    Mass Spectrometry Workflow Orchestration · holobiomicslab

    Use when you have a collection of mzML or mzML.gz files from LC-IMS-MS/MS experiments and need to apply a consistent, reproducible sequence of feature detection, alignment, CCS calibration, isotope detection, and MS/MS deconvolution operations across multiple samples.
    0 installs
54. ▌
    Mass Spectrum Prediction Neural Networks · holobiomicslab

    Use when when you have molecular structures (SMILES, InChI, or chemical formula) and need to predict their tandem mass spectra for structural elucidation or compound ranking against databases. Use SCARF when operating at the chemical formula level;
    2 installs
55. ▌
    Mass To Charge Matching Tolerance Tuning · holobiomicslab

    Use when you are preparing to align two or more nontargeted LCMS datasets from the same analytical method using Eclipse and need to determine the m/z tolerance window.
    0 installs
56. ▌
    Metabolic Model Constraint Specification · holobiomicslab

    Use when you have a generic constraint-based metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, YSI or bioanalyzer extracellular flux measurements) for multiple biological samples and need to create sample-specific models that discriminate whether.
    0 installs
57. ▌
    Metabolite Abundance Threshold Filtering · holobiomicslab

    Use when you have intracellular metabolomics data paired with constraint-based metabolic model predictions and need to identify metabolically controlled reactions.
    2 installs
58. ▌
    Metabolite Edge Scoring Dbedges Bioedges · holobiomicslab

    Use when you have a measured m/z value from spatially-resolved metabolomics or mass spectrometry imaging and need to assign a molecular formula with high confidence. Use it specifically when you have access to a pre-constructed formula network (KnownSet database) linking 2.
    2 installs
59. ▌
    Metabolite Feature Treemap Visualization · holobiomicslab

    Use when after applying mpactr's filter suite (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a peak table, use this skill when you need to summarize the overall filtering outcome across all ion categories and present a compact, area-proportional view of which ions passed.
    0 installs
60. ▌
    Metabolite Mass To Charge Ratio Matching · holobiomicslab

    Use when you have a negative-mode or positive-mode LC-MS feature table with observed m/z values and peak intensities, and you need to identify which metabolites (by KEGG ID) are likely represented.
    0 installs
61. ▌
    Metabolite Pubchemcid Annotation Mapping · holobiomicslab

    Use when after metabolite annotation has been completed (level-1 confidence via spectral library matching in margheRita or equivalent), and you need to perform pathway enrichment analysis on a subset of significant features (e.
    0 installs
62. ▌
    Metabolomic Feature Retention Statistics · holobiomicslab

    Use when after applying the CV_ratio() filtering function to a normalized metabolomic feature matrix (e.g., Urine_RP_NEG_norm.txt) in margheRita, generate retention statistics to report how many features passed the threshold (CV ratio > 1.0) and characterize the distribution of retained CV ratios.
    0 installs
63. ▌
    Metabolomic Feature Table Interpretation · holobiomicslab

    Use when after quality control, filtering, and normalization of an MS-DIAL-derived feature abundance matrix (e.g., Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt), when you have samples assigned to discrete experimental classes (e.
    0 installs
64. ▌
    Missing Value Imputation In Metabolomics · holobiomicslab

    Use when after feature extraction and quality control filtering (blank masking, sample dropping, normalization) have been applied, but before statistical analysis or machine learning.
    0 installs
65. ▌
    Molecular Formula Inference From Adducts · holobiomicslab

    Use when when you have grouped features consolidated into empirical compounds (EmpCpds) with inferred adduct assignments from khipu, and need to perform MS1-level annotation by matching neutral formulas against JMS-compliant reference libraries (HMDB, LMSD).
    0 installs
66. ▌
    Molecular Network Annotation Integration · holobiomicslab

    Use when you have a GNPS mass spectral molecular network (classical or feature-based) and MS2LDA-derived Mass2Motif data, and you need to annotate network nodes with both chemical class information from GNPS library matches and substructural motifs from MS2LDA to enable joint interpretation of.
    0 installs
67. ▌
    Molecular Structure Graph Representation · holobiomicslab

    Use when when you have a set of chemical structures (SMILES strings or SDF files) that need to be processed for training a graph neural network model on molecular property prediction tasks, specifically when the target property (e.
    0 installs
68. ▌
    Ms Ms Fragment Assignment And Annotation · holobiomicslab

    Use when when you have predicted MS/MS fragments from quantum chemistry calculations on N-Me derived unsaturated sterol structures and need to map each fragment to its precursor lipid, calculate exact m/z values, estimate relative intensities, and produce a machine-readable reference table for.
    0 installs
69. ▌
    Multi Hypothesis Scoring And Enumeration · holobiomicslab

    Use when when you have an unknown tandem mass spectrum (MS/MS peaks with m/z and intensity) and need to assign both the precursor chemical formula and its ionization adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+).
    0 installs
70. ▌
    Multi Sample Abundance Pattern Detection · holobiomicslab

    Use when after initial retention-time-based feature grouping (e.
    0 installs
71. ▌
    Multivariate Statistical Quality Control · holobiomicslab

    Use when after data normalization (Step 7) when you have a preprocessed feature matrix and need to identify samples that deviate significantly from the multivariate center of the data distribution due to instrumental drift, batch effects, sample degradation, or genuine biological outliers that.
    0 installs
72. ▌
    Neural Network Regularization Techniques · holobiomicslab

    Use when when training a deep neural network on paired MS/MS spectra to predict structural similarity scores, especially when the training dataset is moderate-sized (109,734 spectra across 15,062 molecules) and overfitting risk is high.
    3 installs
73. ▌
    Neutral Mass Inference From Ion Ensemble · holobiomicslab

    Use when you have a connected subnetwork of feature ions that have been validated as belonging to the same empirical compound (khipu instance), with isotope and adduct edges assigned, and you need to estimate the true neutral mass M0 rather than relying on any single observed m/z.
    0 installs
74. ▌
    Noise Model Implementation And Selection · holobiomicslab

    Use when when constructing synthetic LC-MS/MS runs in SMITER, you must choose a noise model before calling write_mzml.
    2 installs
75. ▌
    Nontargeted Metabolomics Data Processing · holobiomicslab

    Use when you have raw LC-MS data in vendor or mzML format and need to systematically discover and extract all detectable metabolite features across the full retention time range, without predefined target lists.
    2 installs
76. ▌
    Nucleoside Fragmentation Model Selection · holobiomicslab

    Use when when your input biomolecule is a nucleoside or modified nucleoside (not a peptide) and you are building a synthetic LC-MS/MS run with SMITER.
    0 installs
77. ▌
    Open Modification Peptide Identification · holobiomicslab

    Use when when you have high-resolution tandem mass spectra (query spectra) and need to identify peptides with unanticipated or open modifications (any mass shift on any amino acid position).
    2 installs
78. ▌
    Pathway Activity Decomposition Via Plage · holobiomicslab

    Use when you have a log2-transformed, standardized peak intensity matrix (rows = metabolite features, columns = samples) with compound annotations mapped to curated pathway databases (KEGG, Reactome, or custom metabolite sets), and you need to rank pathways by their activity level while tolerating.
    0 installs
79. ▌
    Pathway Over Representation Analysis Ora · holobiomicslab

    Use when apply ORA after conducting statistical tests (e.
    0 installs
80. ▌
    Peak Prominence Calculation Local Maxima · holobiomicslab

    Use when when processing LC-MS mass tracks (EICs) and you need to identify genuine chromatographic peaks rather than noise artifacts.
    0 installs
81. ▌
    Peptide Spectrum Representation Learning · holobiomicslab

    Use when you have a collection of MS/MS spectra (in mzML or MGF format) and need to group or compare spectra from the same peptide without prior sequence annotation.
    2 installs
82. ▌
    Pfas Candidate Prioritization By Scoring · holobiomicslab

    Use when you have a feature list (containing m/z, retention time, and molecular formula or neutral mass per feature) extracted from LC- or GC-HRMS data in mzML format with data-dependent acquisition, and you need to rank or flag features as likely PFAS compounds to reduce manual review burden in.
    0 installs
83. ▌
    Polynomial Regression Quality Assessment · holobiomicslab

    Use when after fitting a polynomial calibration model to tunemix reference data in DEIMoS, assess whether the model explains sufficient variance in the m/z–drift-time–CCS relationship.
    0 installs
84. ▌
    Pytorch State Dict Checkpoint Management · holobiomicslab

    Use when when training a multi-component deep learning model where some components (e.g., a pretrained TCN spectrum encoder) should remain frozen while others (e.
    2 installs
85. ▌
    Qc Replicate Identification And Grouping · holobiomicslab

    Use when you have a QC-annotated LC-MS feature table (CSV or data frame format with sample metadata) and need to isolate QC replicate measurements prior to computing quality metrics such as D-Ratio or performing signal drift correction.
    2 installs
86. ▌
    Retention Time Intensity Data Extraction · holobiomicslab

    Use when you have xcms-processed LC-MS data with detected misaligned feature groups and need to recover the underlying raw retention time–intensity profiles for each feature and sample combination prior to realignment.
    2 installs
87. ▌
    Retention Time Prediction Chromatography · holobiomicslab

    Use when you have a new chromatographic dataset with molecular structures (as InChI or SMILES) and experimentally measured retention times, and you want to predict retention times for unannotated metabolites or validate predictions on a held-out test set without retraining from scratch.
    0 installs
88. ▌
    Retention Time Window Tolerance Checking · holobiomicslab

    Use when you have acquired LC-MS data and need to verify run quality before proceeding to metabolite identification or quantification. Retention time checking is essential when: (1) you have established expected retention time ranges for known internal standards or reference compounds;
    2 installs
89. ▌
    Ripp Peptide Identification From Spectra · holobiomicslab

    Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format) and either raw genome nucleotide sequences or antiSMASH/BOA genome mining tool output, and you need to identify which RiPPs are present in your sample.
    0 installs
90. ▌
    Robust Statistical Spread Quantification · holobiomicslab

    Use when after drift correction of LC-MS peak intensity data, when you need to identify metabolic features with excessive internal spread (within-group variability in QC samples) or poor biological-to-technical reproducibility (QC-versus-sample spread).
    0 installs
91. ▌
    Siamese Network Inference Spectrum Pairs · holobiomicslab

    Use when you have a collection of preprocessed tandem mass spectra (binned into 10,000 equally-sized m/z bins, intensities square-root transformed, top 1,000 peaks retained), a trained MS2DeepScore Siamese model, and you need to predict structural similarity scores (Tanimoto or Dice) for all or a.
    2 installs
92. ▌
    Similarity Matrix Generation And Storage · holobiomicslab

    Use when when you have cleaned and filtered mass spectrometry spectral data (in mzML, mzXML, msp, MGF, or JSON format) and need to identify or rank spectra by similarity for library matching, metabolite annotation, or network analysis.
    2 installs
93. ▌
    Smiles Structure Representation Handling · holobiomicslab

    Use when you have generated a TPs object (via generateTPs) containing transformation products with structural information and need to export these structures for MetFrag database creation, suspect screening list construction, or chemical similarity filtering.
    0 installs
94. ▌
    Spectral Cluster Connectivity Assessment · holobiomicslab

    Use when after running spectral networking on tandem MS data and obtaining a network graph, when you need to assess which spectra cluster together, determine cluster representatives, and propagate RiPP identifications across clusters at distance 1 or 2 to enlarge the set of identified RiPPs beyond.
    0 installs
95. ▌
    Spectral Feature Annotation And Labeling · holobiomicslab

    Use when you have a detected feature table (m/z, drift_time, retention_time, intensity) and need to identify and label C13 isotopic clusters for singly-charged features (z=+1).
    0 installs
96. ▌
    Spectral Library Query Reference Pairing · holobiomicslab

    Use when when evaluating a trained spectral embedding model on publicly available datasets (GNPS, MoNA, MTBLS1572, MassBank, or MassSpecGym) and you need to report averaged performance metrics with standard deviation to demonstrate robustness and reproducibility.
    0 installs
97. ▌
    Spectral Peak Alignment With Mass Offset · holobiomicslab

    Use when when comparing two MS/MS spectra where the precursor m/z values differ (indicating potential mass modifications, adducts, or related compounds), and you want to detect structurally conserved fragmentation patterns that would be missed by direct m/z matching.
    0 installs
98. ▌
    Spectral Peak Smoothing Artifact Removal · holobiomicslab

    Use when raw Agilent MassHunter (.d) or UIMF mass spectrometry files exhibit jagged or noisy peaks, particularly for low-abundance ions where signal-to-noise ratio is poor.
    0 installs
99. ▌
    Spectral Similarity Network Construction · holobiomicslab

    Use when after acquiring MS/MS spectral data from untargeted metabolomics experiments and having candidate transformed structures from biotransformation rule application.
    0 installs
100. ▌
     Spectrum Preprocessing And Normalization · holobiomicslab

     Use when you have raw MS/MS spectra in MGF or other standard formats that need to be ingested into a machine learning pipeline for cross-modal matching against molecular structures, or when spectra from different collision energy levels or instruments require standardization before comparative.
     0 installs