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HolobiomicsLab

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1. ▌
   Open Source Mass Spectrometry File Format Interoperabili 2 · holobiomicslab

   Use when when working with Bruker .d/.baf mass spectrometry imaging data and needing to feed it into MSIGen or other open-source MSI processing pipelines.
   0 installs
2. ▌
   Baseline And Noise Level Estimation From Quartile Statis 3 · holobiomicslab

   Use when before peak detection on a composite or individual mass track when you need to filter out low-intensity noise and baseline drift without removing true signal.
   0 installs
3. ▌
   Interactive Mass Spectrometry Plot Generation And Annota 2 · holobiomicslab

   Use when when you have extracted ion chromatograms (XICs), ion mobilograms (IMs), or mass spectra from diaPASEF or other DIA workflows and need to visualize them interactively to inspect peak boundaries, compare MS1 vs MS2 traces, validate feature identifications, or communicate results.
   0 installs
4. ▌
   Ion Chromatogram Mobilogram Visualization And Interpreta 2 · holobiomicslab

   Use when after loading raw diaPASEF or DIA mass spectrometry data (mzML format) and search results (DIA-NN, OpenSwath, or equivalent) to visually inspect extracted ion chromatograms and mobilograms for selected peptide precursors.
   0 installs
5. ▌
   Extraction Parameter Optimization Ppm Retention Time Ion 2 · holobiomicslab

   Use when you are reconstructing targeted ion chromatograms (XIC) and ion mobilograms (IM) from raw diaPASEF data and need to balance sensitivity (wide extraction windows) against specificity (narrow windows that reject interference).
   0 installs
6. ▌
   Xic Marker Annotation 3 · holobiomicslab

   Use when when you have a resolved spectrum file (mzML, mzXML) and need to visualize where MS2 precursor scans occur on an XIC display.
   0 installs
7. ▌
   Ms Ms Spectrum Matching 2 · holobiomicslab

   Use when you have a cleaned and clustered set of LC-MS features (m/z, retention time, MS/MS spectra) from MS-CleanR output and need to assign putative compound identities by matching observed MS/MS fragmentation patterns against reference spectral libraries using HRR-based scoring.
   0 installs
8. ▌
   Msp File Format Parsing 2 · holobiomicslab

   Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign SMILES, retention indices, or combine multiple libraries into a single consolidated MSP file for MS-DIAL.
   0 installs
9. ▌
   Migration Time Extraction 2 · holobiomicslab

   Use when you have OnDiskMSnExp CE-MS objects with known marker compounds (e.g., Paracetamol EOF marker) and need to extract their migration time positions to establish a calibration reference.
   0 installs
10. ▌
    Spectral Database Matching 2 · holobiomicslab

    Use when when you have MS2 .mzML format data files from untargeted metabolomics or proteomics experiments and need to perform an initial annotation step by matching experimental spectra against known reference libraries (GNPS, HMDB, MassBank) with a defined precursor mass tolerance (e.g., 15 ppm).
    0 installs
11. ▌
    Metabolite To Gene Mapping 3 · holobiomicslab

    Use when you have metabolomic data (e.g., from LC-MS or GC-MS comparing patient to controls) showing differential abundant metabolites (DAMs), candidate genes from exome sequencing or variant calling, and access to a protein–protein or gene–gene interaction network (e.g., STRING).
    0 installs
12. ▌
    Qc Failure Event Detection 2 · holobiomicslab

    Use when rapid QC-MS is actively monitoring LC-MS data acquisition and a QC check result (e.g., internal standard retention time drift, m/z deviation, or intensity threshold breach) returns a fail status.
    1 install
13. ▌
    Spectral Query Formulation 3 · holobiomicslab

    Use when you have a query mass spectrum (or representative metabolite spectrum from public data) and need to identify it by searching against large spectral reference databases (millions to billions of spectra).
    0 installs
14. ▌
    Metabolite Score Projection 2 · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics assay output (metabolite concentrations in a samples × features matrix) and you want to compute a published metabolic risk score or surrogate biomarker (mortality risk, metabolic age, cardiovascular event risk, type-2 diabetes risk, COVID-19.
    0 installs
15. ▌
    Spectral Similarity Scoring 3 · holobiomicslab

    Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g., PNNLMetV20191015.MSL) to identify the unknown compound.
    0 installs
16. ▌
    Drift Time Filtering 2 · holobiomicslab

    Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time chemical noise, high-drift-time tail artifacts, or off-scale ion signals that would degrade subsequent alignment and peak.
    0 installs
17. ▌
    Compound Identifier Mapping 2 · holobiomicslab

    Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and MS/MS spectra ready for annotation.
    0 installs
18. ▌
    Lipid Feature Normalization 3 · holobiomicslab

    Use when after raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate statistical analysis to identify differential lipids and metabolites.
    0 installs
19. ▌
    Mass Chromatogram Alignment 2 · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data, when you have detected features (peaks) in multiple samples and need to establish which peaks across samples represent the same molecular species.
    0 installs
20. ▌
    Matlab Scientific Computing 2 · holobiomicslab

    Use when you have mass spectrometry data in mzXML or mzML format and need to systematically extract regions of interest (ROIs) from multi-dimensional m/z-intensity-time arrays, normalize feature values, and augment datasets for untargeted metabolomics workflows.
    0 installs
21. ▌
    Msflo Metabolite Annotation 2 · holobiomicslab

    Use when after MS-DIAL has completed feature detection and peak alignment on .mzML LC-HRMS data, producing an aligned feature table. Use MSFLO when you need to assign metabolite identities to detected features and filter results by significance criteria before downstream interpretation.
    0 installs
22. ▌
    Mzml File Format Generation 2 · holobiomicslab

    Use when when you need to generate reproducible synthetic LC/GC-MS raw data files with known ground-truth peak properties (m/z, retention time, intensity) for benchmarking peak detection, feature extraction, normalization, or batch correction algorithms;
    0 installs
23. ▌
    Network Topology Comparison 2 · holobiomicslab

    Use when after executing a molecular networking workflow on GC-MS data that has been processed through auto-deconvolution, and a published reference network exists from a prior analysis of the same or analogous dataset.
    0 installs
24. ▌
    Smiles Structure Annotation 2 · holobiomicslab

    Use when you have LC–QTOF mass spectra from real environmental or biological samples (e.g., wastewater, complex mixtures) and need to assign molecular structures to spectra where traditional library matching fails or reference compounds are unavailable.
    0 installs
25. ▌
    Vendor Data Standardization 2 · holobiomicslab

    Use when you have raw MS data files directly from a vendor instrument (Thermo .raw, Agilent .d, Waters .ms, etc.) and need to process them through AriumMS or any other metabolomics pipeline that accepts only .mzXML or .mzML formats.
    0 installs
26. ▌
    Baseline Comparison Analysis 2 · holobiomicslab

    Use when when you have trained a candidate model (e.g., an ensemble, a new architecture) and need to demonstrate its advantage over published or reference implementations on the same test data.
    0 installs
27. ▌
    Gc Ms Spectral Deconvolution 2 · 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.
    0 installs
28. ▌
    Isotopic Impurity Accounting 2 · holobiomicslab

    Use when when analyzing LC-MS data from stable isotope labeling experiments where measured isotopologue abundances are contaminated by naturally occurring isotopes and tracer isotopic impurity, and you have access to unlabeled sample reference measurements to empirically model these confounding.
    0 installs
29. ▌
    Metabolite Spectral Matching 3 · holobiomicslab

    Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference spectra in GNPS or a local indexed repository.
    0 installs
30. ▌
    Spectral Peak Shape Modeling 2 · holobiomicslab

    Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each peak while accounting for chromatographic band broadening, peak tailing, and retention-time dispersion.
    0 installs
31. ▌
    Stocsy Metabolite Assignment 3 · holobiomicslab

    Use when use STOCSY when you have preprocessed 1H NMR spectral data with an unidentified peak of interest (driver signal at a specific δ ppm value) and need to determine its metabolite identity by finding correlated signals across the spectrum.
    0 installs
32. ▌
    Mass Spectral Data Validation 2 · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
    0 installs
33. ▌
    Annotation Confidence Scoring 3 · holobiomicslab

    Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final annotated metabolite identities.
    0 installs
34. ▌
    Coeluting Compound Resolution 2 · holobiomicslab

    Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw chromatogram.
    0 installs
35. ▌
    Gc Ms Chromatogram Processing 2 · holobiomicslab

    Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against reference libraries such as PNNLMetV20191015.MSL.
    0 installs
36. ▌
    Level 4 Annotation Assignment 2 · holobiomicslab

    Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
    0 installs
37. ▌
    Metabolite Cluster Evaluation 2 · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to cross-validate the two available scoring methods (findMain and RAMClustR internal scoring) to identify cases where they.
    0 installs
38. ▌
    Metabolomic Feature Alignment 2 · holobiomicslab

    Use when you have two or more CSV feature tables from independent metabolomic experiments (each with RT, m/z, intensity, isotope, and adduct columns), and you need to merge them into a single aligned feature matrix for downstream batch effect removal, marker identification, or pathway analysis.
    0 installs
39. ▌
    Multi Platform Ms Integration 3 · holobiomicslab

    Use when you have untargeted metabolomics data from multiple MS instruments (e.
    0 installs
40. ▌
    Spectral Graph Interpretation 2 · holobiomicslab

    Use when after submitting MS/MS data and feature tables to GNPS and receiving a molecular networking job result.
    0 installs
41. ▌
    Tandem Ms Data Reorganization 2 · holobiomicslab

    Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment fields rather than in dedicated SMILES/InChIKey fields, or when positive and negative ionization mode spectra are commingled.
    0 installs
42. ▌
    Spectral Library Matching Gnps 3 · holobiomicslab

    Use when you have MS2 product-ion spectra in open formats (.mzML or .mzXML) from public mass spectrometry datasets (e.g., from MassIVE with a valid accession) and need to identify chemical compounds by comparing fragmentation patterns against the GNPS reference spectral library.
    0 installs
43. ▌
    Dia File Format Parsing 2 · holobiomicslab

    Use when you have raw DIA mass spectrometry files in timsTOF (.d), TripleTOF (.wiff), or Orbitrap (.raw) format and need to extract precursor ion chromatogram (PIC) data as input for quality metric computation or machine learning-based file quality prediction.
    0 installs
44. ▌
    Hdf5 File Io Operations 2 · holobiomicslab

    Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS calibration), or when you need to export annotated feature tables with isotopologue metadata back to HDF5 for archival.
    0 installs
45. ▌
    Mass Accuracy Alignment 2 · holobiomicslab

    Use when after parsing MRM transition tables (m/z values, retention times, transition parameters) from mzML data, before statistical analysis or visualization. Use this skill when you have detected but unannotated transitions and need to map them to lipid species with quantified confidence.
    0 installs
46. ▌
    Module Coverage Mapping 2 · holobiomicslab

    Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation techniques.
    0 installs
47. ▌
    Xcms Workflow Execution 2 · holobiomicslab

    Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the cohort.
    0 installs
48. ▌
    Annotation Scoring And Ranking 2 · holobiomicslab

    Use when you have experimental mass spectra from untargeted metabolomics and need to assign compound identities with confidence estimates.
    0 installs
49. ▌
    Chromatographic Noise Modeling 2 · holobiomicslab

    Use when you need to generate blank or background-only .mzML files for method validation, when you want to create synthetic negative controls with realistic instrumental noise but no analyte peaks, or when you need to simulate serum matrix background (e.
    0 installs
50. ▌
    Data Augmentation Metabolomics 2 · holobiomicslab

    Use when you have preprocessed and normalized ROI feature data extracted from mzXML or mzML mass spectrometry files and seek to increase feature representation and robustness before statistical modeling or machine learning.
    0 installs
51. ▌
    Gaussian Peak Shape Evaluation 3 · 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.
    0 installs
52. ▌
    Imputation Algorithm Selection 3 · holobiomicslab

    Use when you have a metabolomics dataset with left-censored missing values (e.g., below limit of quantification in LC/MS or GC/MS) and need to evaluate multiple imputation approaches.
    0 installs
53. ▌
    Mass Spectral Query Submission 2 · holobiomicslab

    Use when you have one or more individual MS/MS spectra (in mzML, mzXML, or JSON format) and need to identify the compound(s) and their biological source by searching against a domain-specific spectral library.
    0 installs
54. ▌
    Modification Site Localization 3 · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally related modified (unknown) compound—and need to identify which atom(s) in the structure carry the modification.
    0 installs
55. ▌
    Mona Metadata Field Extraction 2 · holobiomicslab

    Use when when you have loaded a MoNA mass spectral library (GC-MS or LC-MS/MS) in MSP format and observe that SMILES strings are present in the Comment field rather than in a dedicated SMILES metadata field.
    0 installs
56. ▌
    Ranking Task Loss Optimization 2 · holobiomicslab

    Use when you have multiple pre-trained neural network models (e.g., MLP and GNN) that produce overlapping predictions on the same set of candidates, and your evaluation metric is rank-based (average rank, Rank@K) rather than point-wise accuracy or RMSE.
    0 installs
57. ▌
    Candidate Formula Ranking 3 · holobiomicslab

    Use when you have an observed m/z value from mass spectrometry imaging and need to assign a chemical formula with high confidence.
    0 installs
58. ▌
    Signal Quality Assessment 2 · holobiomicslab

    Use when you have imported raw MSI spectral data in imzML format and need to improve signal-to-noise ratio before performing mean intensity calculations, ROI analysis, or database annotation.
    0 installs
59. ▌
    Neural Network Model Deployment 2 · 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.
    0 installs
60. ▌
    Retention Time Filtering 2 · holobiomicslab

    Use when working with GCIMS datasets where retention time spans a wide range (e.g., 0–1500 s) but your analytes of interest are confined to a narrower window (e.g., 0–1100 s).
    1 install
61. ▌
    Spectral Noise Filtering 3 · holobiomicslab

    Use when immediately after extracting ion chromatograms (EICs) by binning mass spectral data across the full m/z range from raw LC/HRMS files (mzML, mzXML, or netCDF format).
    0 installs
62. ▌
    Centroided Ms Feature Detection 2 · holobiomicslab

    Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.
    0 installs
63. ▌
    Dysregulation Score Computation 2 · holobiomicslab

    Use when you have per-sample metabolite abundance data (e.g., from LC-MS or GC-MS) and a metabolite-to-pathway assignment table, and need to generate a sample-by-pathway dysregulation matrix for downstream classification, prognosis prediction, or pathway-level phenotype association.
    0 installs
64. ▌
    Metabolite Structure Prediction 3 · holobiomicslab

    Use when you have a parent compound (or set of compounds) in SMILES, MOL, or SDF format and need to predict plausible metabolite structures and pathways in a specific biological context (mammalian Phase I/II metabolism, human gut microbiota, or soil/aquatic microbial degradation).
    0 installs
65. ▌
    Raw Chromatography Data Parsing 2 · 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.
    0 installs
66. ▌
    Roi Detection Mass Spectrometry 2 · holobiomicslab

    Use when you have raw or converted mass spectrometry data (CE-MS or LC-MS in mzXML or mzML format) and need to identify candidate metabolite regions before feature extraction.
    0 installs
67. ▌
    Xcms Parameter Optimization Msw 2 · holobiomicslab

    Use when when you have direct-injection or low-complexity mass spectrometry data (mzML files) and need to detect chromatographic peaks using wavelet-based methods instead of centWave, especially when standard retention-time-dependent peak detection is not suitable or when you need to tune.
    0 installs
68. ▌
    Ms Ms Raw Data Loading 2 · holobiomicslab

    Use when when you have raw LC-MS/MS instrument output files (e.g., .mzML, .
    0 installs
69. ▌
    Metabolite Identifier Annotation 3 · holobiomicslab

    Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by comparing them to computationally predicted metabolism pathways.
    0 installs
70. ▌
    Imzml File Format Parsing 2 · holobiomicslab

    Use when you have acquired imaging mass spectrometry (IMS) data stored in imzML format (accompanied by an .ibd ion binary data file) and need to load it into a Python-based spatial metabolomics workflow.
    0 installs
71. ▌
    Ion Mobility Peak Picking 2 · holobiomicslab

    Use when when you have extracted ion mobilograms from DIA-MS experiments and need to automatically identify peak boundaries and apex positions in the ion mobility dimension.
    0 installs
72. ▌
    Spatial Feature Embedding 3 · holobiomicslab

    Use when when analyzing imaging mass spectrometry datasets where you need to reduce high-dimensional peak intensity features while preserving spatial structure, and when automatic peak picking and marker ion identification are required.
    0 installs
73. ▌
    Annotation Confidence Assessment 2 · holobiomicslab

    Use when after MS-FINDER in silico annotation has been executed on exported LC-MS features and multiple database matches (with HRR scores) have been returned.
    0 installs
74. ▌
    Chemical Mass Tolerance Matching 2 · holobiomicslab

    Use when when you have a metabolomics peak list (m/z values with optional retention times) from LC-MS or GC-MS and want to filter a computationally expanded chemical library to only compounds whose calculated masses (accounting for ionization adducts) fall within a defined tolerance of observed.
    0 installs
75. ▌
    Fticr Mass Calibration Edgeshift 2 · holobiomicslab

    Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.
    0 installs
76. ▌
    Mass Spectrometry Data Alignment 2 · holobiomicslab

    Use when you have two LC-MS feature tables (each containing m/z, retention time, and intensity columns) from the same or related biological samples and need to identify which features in dataset A correspond to which features in dataset B.
    0 installs
77. ▌
    Metabolomics Data Representation 2 · holobiomicslab

    Use when you have a raw MGF file containing fragmented LC-MS-MS metabolomics spectra and want to apply Latent Dirichlet Allocation (LDA) to discover hidden topics (molecular families, biochemical patterns) across your sample set.
    0 installs
78. ▌
    Metabolomics Matrix Manipulation 3 · holobiomicslab

    Use when you have a raw metabolomics abundance table (e.g., LC/MS or GC/MS peak intensities or concentrations) with non-normal distributions and missing values, and you need to prepare it for Gibbs sampler or other model-based imputation.
    0 installs
79. ▌
    Qc Sample Batch Drift Correction 2 · holobiomicslab

    Use when you have a QC-annotated feature table (samples × features with QC sample identifiers) from LC-MS untargeted metabolomic profiling and observe systematic signal drift across the run sequence or between batch blocks.
    1 install
80. ▌
    Singularity Container Deployment 2 · holobiomicslab

    Use when you have a Nextflow workflow (e.g., Nextflow4MS-DIAL) that currently runs under Docker or bare metal, and you need to execute it on an HPC cluster that lacks Docker support or enforces Singularity as the container runtime.
    0 installs
81. ▌
    Spectral Prediction Model Fusion 2 · holobiomicslab

    Use when you have pre-trained MLP and GNN spectral prediction models evaluated on the same ESI/LC-MS test dataset, and you seek to improve average rank performance beyond either baseline model alone.
    0 installs
82. ▌
    Spectral Roi Boundary Definition 2 · holobiomicslab

    Use when when you have identified a spectral window of interest in a 1H NMR spectrum from a complex biological sample (serum, urine, CSF, tissue, saliva, or sweat) and need to systematically retrieve all metabolites from HMDB whose reference proton NMR chemical shifts fall within that window.
    0 installs
83. ▌
    Mass Accuracy Ppm Filtering 3 · holobiomicslab

    Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
    0 installs
84. ▌
    R Data Structure Conversion 2 · holobiomicslab

    Use when you have preprocessed MSI data in Cardinal format (post-peakBin) and need to apply mass2adduct's adduct-detection workflow, OR you have exported MSI intensity data as CSV from third-party software (SCiLS, MSiReader) and must convert it into a standardized R object for downstream analysis.
    0 installs
85. ▌
    Mztab Format Generation 2 · holobiomicslab

    Use when after completing peak detection, MS1 feature picking, and accurate mass database search (e.g., against HMDB) on FIA-MS or LC-MS(/MS) data.
    0 installs
86. ▌
    Metabolite Signal Drift Detection 2 · holobiomicslab

    Use when when you have multi-batch metabolomics data (SummarizedExperiment object with raw or log-transformed assays) and need to assess whether specific metabolites exhibit systematic signal drift across experimental run order or strong batch effects that would justify hierarchical normalisation.
    0 installs
87. ▌
    Small Molecule Structure Matching 3 · holobiomicslab

    Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the observed compounds by matching their experimental features (mass-to-charge ratio, retention time, spectral signature) to.
    0 installs
88. ▌
    Lcms Feature Table Parsing 2 · holobiomicslab

    Use when you have raw nontargeted LCMS feature tables from one or more analytical methods in tabular format (with m/z, RT, and intensity columns) that need to be aligned or clustered, or when integrating multiple feature tables into a shared BMXP processing pipeline that requires standardized.
    0 installs
89. ▌
    Sample Membership Tracking 2 · holobiomicslab

    Use when when aligning detected features across multiple LC-IMS-MS/MS samples and you need to identify which input samples contributed to each consensus feature cluster, especially to filter out spurious or low-confidence alignments, validate clustering completeness, or perform sample-specific.
    0 installs
90. ▌
    Spectral Window Extraction 2 · holobiomicslab

    Use when you have loaded multidimensional MS data (from MZA HDF5 files or other formats) and need to examine a specific m/z region—for example, to visualize a known lipid or metabolite mass range, perform peak detection within a narrow window, or reduce computational overhead by working on a subset.
    0 installs
91. ▌
    Carbon Oxidation State Assessment 2 · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peak data, when you need to classify metabolites by their redox state to predict bioavailability or lability, or when generating thermodynamic indices for chemodiversity analysis and environmental metabolomic interpretation.
    0 installs
92. ▌
    Chromatography Data Preprocessing 2 · holobiomicslab

    Use when you have raw spectra files from a liquid chromatography experiment (in-house or external database) and need to adapt a pretrained GNN-RT model to predict retention times for your molecules. Preprocessing is the mandatory first step before any model training or transfer learning can proceed.
    0 installs
93. ▌
    Empirical Compound Pre Annotation 2 · holobiomicslab

    Use when after feature detection from mzML files (e.g., via Asari) when you have a feature table with m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
    0 installs
94. ▌
    Ftms Raw Data Loading And Parsing 2 · holobiomicslab

    Use when you have received raw FT-ICR transient data from Bruker Solarix or ThermoFisher instruments and need to perform signal processing, apodization, calibration, or molecular formula assignment in CoreMS. The data must be in native vendor format (.d directory with ser/fid files, or .
    0 installs
95. ▌
    Isotope Labeling Data Integration 3 · holobiomicslab

    Use when you have LC-MS peak tables from parallel unlabeled and labeled (isotope-traced) sample cohorts, sample metadata defining groups and conditions, and you seek to identify metabolic intermediates that accumulate differentially in a perturbed system (e.
    0 installs
96. ▌
    Lcms Metabolomics Data Processing 2 · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .
    1 install
97. ▌
    Multi Database Structure Querying 2 · holobiomicslab

    Use when after cleaning and clustering LC-MS features in MS-CleanR, when you need to assign putative compound identities to a feature set with MS/MS spectra, and when candidate compounds may exist across multiple specialized databases (e.g., natural products, pharmaceuticals, contaminants).
    0 installs
98. ▌
    Mzmine Quantitative Table Parsing 2 · holobiomicslab

    Use when you have LC–MS/MS data processed through MZmine2 or MZmine3 and need to construct a feature quantification table for natural product discovery pipelines (e.g., INVENTA prioritization, GNPS networking, or metabolite annotation).
    0 installs
99. ▌
    Peak Extraction Rescue Algorithms 2 · holobiomicslab

    Use when traditional peak extraction algorithms have produced a feature table that you suspect is incomplete or missing known suspects from your target database (e.g., T3DB).
    0 installs
100. ▌
     Peak Picking Algorithm Comparison 3 · holobiomicslab

     Use when you have claims in a paper or tool documentation that one peak picking method outperforms others (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms'), but the specific comparison metrics, numerical results, and source tables are not provided in the abstract or introduction.
     2 installs