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HolobiomicsLab

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1. ▌
   Spectral Ion Matching Across Vendors 2 · holobiomicslab

   Use when you have raw line-scan MSI data from any supported vendor (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .
   0 installs
2. ▌
   Sterol Lipid Isomer Characterization 3 · holobiomicslab

   Use when you have LC-IM-MS/MS experimental data (raw mzML or vendor format) containing signals from N-Me derived unsaturated sterol lipids and need to assign double-bond positions and stereochemistry to individual sterol isomers rather than sum compositions.
   0 installs
3. ▌
   Baseline Method Comparison And Benchmarking 3 · holobiomicslab

   Use when you have developed or adapted an analytical method (e.g., NPFimg for GC–MS marker identification) and need to demonstrate its reliability or improved performance over a widely-used reference method (e.g., XCMS). Apply this skill when you have access to both the same raw input data (e.
   0 installs
4. ▌
   Mass Spectrometry Scoring Method Validation 2 · holobiomicslab

   Use when you have high-resolution LC-MS data processed through both XCMS feature detection and RAMClustR clustering, and you need to verify the reliability of molecular weight assignments before downstream annotation or statistical analysis.
   0 installs
5. ▌
   Metadata Field Extraction And Restructuring 2 · holobiomicslab

   Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g., Comment field) rather than in the dedicated SMILES field expected by mspcompiler's downstream processing steps.
   0 installs
6. ▌
   Spectral Overview Representation Generation 2 · holobiomicslab

   Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D projection suitable for dashboard visualization or high-level pattern discovery without losing similarity structure.
   0 installs
7. ▌
   Spectral Peak Word Embedding Representation 3 · holobiomicslab

   Use when when you have MS/MS spectra (LC-MS or equivalent positive ionization mode data) that you intend to embed using Word2Vec or similar distributional semantic models, or when you need to prepare spectral data for training similarity models that learn peak co-occurrence patterns rather than.
   0 installs
8. ▌
   Adduct Ion Parent Ion Pairing Analysis 2 · holobiomicslab

   Use when when you have binned mass spectrometry imaging peaks and want to understand which detected mass-to-charge ratios represent the same metabolite in different ionization states (parent vs. adduct form).
   0 installs
9. ▌
   Mass Spectrometry Imaging Data Loading 3 · holobiomicslab

   Use when you have raw or preprocessed MS imaging data archived as an RDS file or from a Zenodo deposit that includes the full m/z feature set (e.g., 10,200 m/z values spanning 150–1000 m/z range) and spectrum count (e.
   0 installs
10. ▌
    Adduct Based Feature Consolidation 2 · holobiomicslab

    Use when after accurate mass searching has assigned multiple detected m/z features to the same metabolite via positive and negative adduct libraries, and before sample-level feature merging.
    0 installs
11. ▌
    Feature Quality Assessment Metrics 3 · holobiomicslab

    Use when after nontargeted peak detection and segmentation has generated a feature table from raw LC-MS data (mzML or vendor format), apply quality assessment when you need to rank or filter features by confidence before annotation, adduct grouping, or MS/MS matching.
    0 installs
12. ▌
    In Silico Fragment M Z Calculation 2 · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS or direct infusion MS/MS data and need to identify lipid species by comparing observed fragment m/z values against a library of simulated fragments. Apply this skill when your lipid library is incomplete or specialized (e.
    0 installs
13. ▌
    Metabolomics Feature Preprocessing 2 · holobiomicslab

    Use when when you have raw profile LC-MS data in .mzML format and need to prepare regions of interest (ROI) as input for a CNN-Transformer peak detection network.
    0 installs
14. ▌
    Multiformat Data Export To PDF CSV 2 · holobiomicslab

    Use when you have raw MS data in vendor formats (Agilent .d, Thermo .raw, Bruker .
    0 installs
15. ▌
    Pure Component Spectrum Extraction 2 · holobiomicslab

    Use when analyzing GC-MS data containing overlapped peaks where two or more components co-elute within the same retention time window, making direct spectral assignment impossible.
    0 installs
16. ▌
    Retention Time Prediction Modeling 2 · holobiomicslab

    Use when you have a set of small-molecule compounds (e.g., from MS/MS library matching or database annotation) that require retention time validation or ranking to resolve ambiguous identifications.
    0 installs
17. ▌
    Bruker Baf Data Import And Conversion 2 · holobiomicslab

    Use when you have Bruker .d/.baf format mass spectrometry imaging data and need to ingest it into MSIGen for conversion to visualizable ion images. This skill applies when your raw data originates from Bruker TIMSTOF or similar instruments and you lack direct .
    0 installs
18. ▌
    Compound Structure Comparison Metrics 3 · holobiomicslab

    Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
    0 installs
19. ▌
    Ion Mobility Demultiplexing Algorithm 3 · holobiomicslab

    Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover conventional (non-multiplexed) IM-MS spectra with resolved mobility and mass dimensions.
    0 installs
20. ▌
    Latent Space Dimensionality Reduction 3 · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) datasets where peak intensities are high-dimensional and sparse, and you need to extract compressed latent features that preserve spatial adjacency relationships and enable iterative automatic peak picking to identify marker ions.
    0 installs
21. ▌
    Mass Spectrometry File Format Parsing 2 · holobiomicslab

    Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized bag-of-fragments representation for unsupervised topic modeling or substructure discovery workflows.
    0 installs
22. ▌
    Mass Spectrometry Image Normalization 2 · holobiomicslab

    Use when after loading a pixel array (NumPy format) and its associated metadata JSON file from MSIGen, when you need to account for pixel-to-pixel variations in total ion signal or when comparing relative abundances of multiple ions within or across samples.
    0 installs
23. ▌
    Mass Spectrometry Screening Workflows 2 · holobiomicslab

    Use when when you have high-resolution LC-MS or GC-MS data from environmental samples and need to simultaneously screen for both known suspect chemicals and their transformation products, rather than targeting single compounds.
    0 installs
24. ▌
    Module Dispatch Architecture Analysis 2 · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its declared data type (LC vs. GC vs. IMS vs. MS imaging).
    0 installs
25. ▌
    Multidimensional Coordinate Alignment 2 · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples (each containing m/z, drift_time, retention_time, and intensity measurements) and need to identify which features correspond to the same chemical compound across samples.
    0 installs
26. ▌
    Precursor Ion Chromatogram Extraction 2 · holobiomicslab

    Use when you have raw DIA mass spectrometry data files (.raw, .d, or .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to extract precursor ion chromatograms for quality assessment or downstream analysis.
    0 installs
27. ▌
    Spectral Similarity Scoring Parent Tp 2 · holobiomicslab

    Use when after generating TP candidates (via in-silico prediction or library lookup) and extracting MS/MS peak lists for both parent features and TP feature candidates, use spectral similarity scoring to quantify fragmentation pattern overlap.
    0 installs
28. ▌
    Empirical Compound Construction And Grouping 2 · holobiomicslab

    Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
    0 installs
29. ▌
    Floating Point Numerical Accuracy Assessment 3 · holobiomicslab

    Use when when implementing or validating a lossy numeric codec for mass-spectrometry data (e.g., MSNumpressCoder in OpenMS). Specifically: after implementing both encoder and decoder, before shipping to production, or when comparing alternative compression schemes.
    0 installs
30. ▌
    Gibbs Sampler Implementation And Convergence 3 · holobiomicslab

    Use when your metabolomics dataset contains missing values below a known detection limit (left-censored MNAR data), and you need to recover these values while respecting the truncation constraint.
    0 installs
31. ▌
    Mass Calibration Against Reference Standards 2 · holobiomicslab

    Use when when processing raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d) that requires assignment of molecular formulas to experimental m/z peaks. Calibration is necessary before SearchMolecularFormulas because uncalibrated mass error will cause false formula rejections or incorrect assignments.
    0 installs
32. ▌
    Peak List Simulation With Controlled Effects 2 · holobiomicslab

    Use when you need to validate batch correction or normalization algorithms, require ground-truth condition/batch effect annotations for method benchmarking, or want to systematically evaluate how different batch types (linear, random) and condition allocations affect feature recovery in metabolomic.
    0 installs
33. ▌
    Two Dimensional Chromatography Data Handling 2 · holobiomicslab

    Use when you have raw GCxGC-MS chromatogram data in NetCDF format from multiple samples (e.g., case and control groups) and need to prepare them for multivariate analysis such as multiway principal component analysis (MPCA).
    0 installs
34. ▌
    Word Embedding Aggregation For Spectral Data 3 · holobiomicslab

    Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular networking that correlate better with structural similarity than cosine-based methods.
    0 installs
35. ▌
    Formula Assignment In Mass Spectrometry 3 · holobiomicslab

    Use when you have m/z values from mass spectrometry imaging (or similar MSI experiments) and need to assign molecular formulae to them. This is especially valuable when working with spatially-resolved metabolomics data where annotation precision lags behind traditional LC-MS approaches.
    0 installs
36. ▌
    Network Based Metabolite Identification 3 · holobiomicslab

    Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
    0 installs
37. ▌
    Reconstruction Algorithm Implementation 2 · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry data (feature matrices or transient files) acquired at lower mass resolution or with signal degradation, and you possess high-resolution reference MSI data or simulated ground truth to train a reconstruction model.
    0 installs
38. ▌
    Spatial Metabolomics Feature Annotation 3 · holobiomicslab

    Use when your spatial metabolomics dataset contains raw m/z features (e.g., from MALDI-MS imaging or LC-MS/MS) without metabolite annotations, and you have selected a reference database and adduct type appropriate for your ionization mode and biological sample.
    0 installs
39. ▌
    Peaklist Metabolite Assignment Prioritization 2 · holobiomicslab

    Use when you have extracted m/z and retention time (m/z-RT) information for peaks from untargeted LC/HRMS data (using tools like IDSL.IPA) and need to assign molecular formula identities to those peaks.
    0 installs
40. ▌
    Acquisition Method Overlap Analysis 2 · holobiomicslab

    Use when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS, or direct infusion methods (e.
    0 installs
41. ▌
    Feature Table Export And Formatting 2 · holobiomicslab

    Use when after completing feature detection, alignment, and optional filtering (blank subtraction, QC reproducibility, feature occurrence thresholds) in MZmine2 or Optimus, and you need to prepare the feature table and MS/MS spectra for GNPS-based molecular networking, bioassay integration, or.
    0 installs
42. ▌
    Mass Spectrometry Data File Parsing 2 · holobiomicslab

    Use when you receive raw MS data files from LC-MS, LC-IMS-MS, direct infusion, or DDA/DIA experiments and need to extract ion chromatograms, mobility heatmaps, quality metrics, or perform spectral matching.
    0 installs
43. ▌
    Mass Spectrometry Outlier Detection 2 · holobiomicslab

    Use when you have multi-sample MS1 data (LC-MS, LC-IMS-MS, or direct infusion across any omics domain) and need to detect samples with abnormal global ion intensity patterns or unusual per-ion metric behavior (intensity distribution, signal-to-noise, retention time stability) that may indicate.
    0 installs
44. ▌
    Adduct Fragment Formula Interpretation 2 · holobiomicslab

    Use when after temporal correlation has identified candidate feature pairs with matching intensity profiles across time-resolved DBDI-MS experiments.
    0 installs
45. ▌
    Data Type Classification Schema Design 2 · holobiomicslab

    Use when building or auditing a multi-instrument MS data processing system that must route different chromatography modes (LC, GC), ion mobility, or imaging modalities (MALDI) to distinct processing workflows.
    0 installs
46. ▌
    Distance Clustering In High Dimensions 2 · holobiomicslab

    Use when when you have detected feature tables from two or more LC-IMS-MS/MS samples and need to establish correspondence between features across samples (i.e., which features in sample A match which features in sample B).
    0 installs
47. ▌
    Drift Time To Ccs Correlation Modeling 2 · holobiomicslab

    Use when you have tunemix or other reference standards with known m/z, drift-time, charge state, and CCS values, and you need to establish a predictive calibration model for your ion-mobility mass spectrometry instrument.
    0 installs
48. ▌
    Ion Mode Specific Ccs Model Generation 2 · holobiomicslab

    Use when you have tunemix reference data acquired in both positive and negative ion modes and need to establish independent CCS calibration curves for each mode. The skill is required when downstream CCS assignments must achieve R² ≥ 0.
    0 installs
49. ▌
    Lipid Identification Quality Filtering 2 · holobiomicslab

    Use when you have MS-DIAL lipid identification results (alignment exports in msp/txt format) and need to distinguish correct from incorrect lipid IDs before downstream analysis.
    0 installs
50. ▌
    Molecular Database Loading And Parsing 2 · holobiomicslab

    Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1 only) before generating virtual LC-MS/MS data.
    0 installs
51. ▌
    Multidimensional Signal Smoothing Imms 3 · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains jagged, low-abundance ion peaks or when saturation repair has been applied and the resulting reconstructed signals need artifact removal and enhancement.
    0 installs
52. ▌
    Pixel Binning And Spatial Registration 2 · holobiomicslab

    Use when you have raw line-scan mass spectrometry imaging data from nano-DESI or other line-scan acquisition modes and need to produce a georeferenced 3D pixel array.
    0 installs
53. ▌
    Retention Time Drift Time M Z Querying 2 · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format and need to retrieve specific spectra or chromatographic slices defined by one or more of: retention time (in minutes), ion mobility arrival time (in milliseconds for DT/SLIM or Vs/cm² for TimsTOF), or m/z value (as a float or.
    0 installs
54. ▌
    Snakemake Dag Generation And Execution 2 · holobiomicslab

    Use when you have multiple mzML or mzML.gz files from LC-IMS-MS/MS instruments and need to apply DEIMoS feature detection, alignment, and calibration operations in a reproducible, traceable manner.
    0 installs
55. ▌
    Large Scale All Pairs Similarity Benchmarking 3 · holobiomicslab

    Use when you have multiple competing spectral similarity scoring methods (e.
    0 installs
56. ▌
    Multi Batch Experimental Design Understanding 2 · holobiomicslab

    Use when your metabolomics experiment includes samples acquired across multiple instrument runs, different preparation dates, or distinct sample cohorts.
    0 installs
57. ▌
    Pfas Characteristic Mass Difference Detection 2 · holobiomicslab

    Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
    0 installs
58. ▌
    R Workflow Scripting For Analytical Chemistry 2 · holobiomicslab

    Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration times, m/z values, peak intensities) by orchestrating multiple R packages in a controlled, documented sequence.
    0 installs
59. ▌
    Retention Index Extraction From Nist Database 2 · holobiomicslab

    Use when you have a compiled EI or MS2 library object (from read_lib or c() combination of multiple sources) and a local NIST library installation with accessible ri.dat and USER.DBU files in the mssearch/nist_ri directory.
    0 installs
60. ▌
    Word2vec Embedding Training Mass Spectrometry 3 · holobiomicslab

    Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture fragmentation patterns and neutral loss relationships.
    0 installs
61. ▌
    Metabolite Edge Scoring Dbedges Bioedges 3 · 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.
    0 installs
62. ▌
    Lipid Feature Annotation And Sorting 3 · holobiomicslab

    Use when after quantifying ion images in LipidQMap and before exporting to HDF5 format, when you need to organize per-feature metadata (lipid ID, class, adduct, m/z, internal standard flag) into aligned datasets that can be linked to intensity data via dimension scales and sorted for reproducible.
    0 installs
63. ▌
    Mass Difference Network Construction 3 · holobiomicslab

    Use when you have a preprocessed peak list (m/z values and assigned molecular formulas) from direct injection FT-ICR MS of a complex organic mixture (e.
    0 installs
64. ▌
    Ms1 Feature Detection And Annotation 2 · holobiomicslab

    Use when you have FIA-MS, LC-MS, or GC-MS full-scan data in mzML format and need to identify unknown molecular features by accurate mass.
    0 installs
65. ▌
    Spatial Correlation Filtering In Msi 2 · holobiomicslab

    Use when after identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular adducts from coincidental mass matches.
    0 installs
66. ▌
    Chromatographic Modality Classification 2 · holobiomicslab

    Use when when ingesting raw or vendor-format mass spectrometry data files of unknown or mixed acquisition modality, and you need to automatically determine whether the input originated from liquid chromatography (LC), gas chromatography (GC), ion mobility spectrometry (IMS), or MS imaging (e.
    0 installs
67. ▌
    Collision Cross Section Calibration Ccs 2 · holobiomicslab

    Use when when you have acquired ion mobility–mass spectrometry data (drift time and m/z dimensions) and need to convert observed drift times into calibrated CCS values.
    0 installs
68. ▌
    Fragmentation Pattern Spectral Matching 3 · holobiomicslab

    Use when when you have detected m/z values from LC-IM-MS/MS that match a candidate CCS prediction database but require structural confirmation. Apply this skill to disambiguate isomers (e.
    0 installs
69. ▌
    Instrument Agnostic Feature Engineering 2 · holobiomicslab

    Use when you have DIA raw mass spectrometry files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) and need to build a single machine learning model to predict data quality across all platforms, or when you need to compare quality characteristics of files produced by different.
    0 installs
70. ▌
    Internal Standard Intensity Calibration 2 · holobiomicslab

    Use when you have added a known internal standard compound to your nano-DESI MSI sample and want to correct for pixel-to-pixel variation in ionization efficiency or sample deposition.
    0 installs
71. ▌
    Lipid Derivatization Chemistry Modeling 3 · holobiomicslab

    Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before experimental acquisition, or to build a reference spectral library for isomer-level sterol identification in tissue samples.
    0 installs
72. ▌
    Mass Spectrometry Data Table Formatting 2 · holobiomicslab

    Use when when you have raw or processed TWIM-MS data (arrival time and m/z values) from a mass spectrometry instrument and need to organize it into a feature table before biomolecular class assignment or CCS calculations.
    0 installs
73. ▌
    Ms Spectrum Filtering And Normalization 2 · holobiomicslab

    Use when you have raw or parsed tandem MS spectra (MGF, mzML, or in-memory Spectrum objects) and need to remove artifacts and normalize intensities prior to spectral matching, library searching, or downstream analysis.
    0 installs
74. ▌
    Peak Integration Parameter Optimization 2 · holobiomicslab

    Use when after peak detection and clustering have been completed on aligned and baseline-corrected GC-IMS data, and before imputation or statistical analysis.
    0 installs
75. ▌
    Peptide Sequence To Spectrum Conversion 2 · holobiomicslab

    Use when when you have a peptide sequence and need to predict its fragmentation pattern under specific isotopic labeling conditions (e.g., natural 13C abundance at 1%, or enriched 13C at arbitrary levels).
    0 installs
76. ▌
    Quantum Chemistry Structure Preparation 3 · holobiomicslab

    Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for LC-IM-MS/MS analysis.
    0 installs
77. ▌
    Separation Technique Workflow Alignment 2 · holobiomicslab

    Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.
    0 installs
78. ▌
    Spectral Peak Binning And Vectorization 2 · holobiomicslab

    Use when you have raw MS/MS spectra with variable numbers of peaks at continuous m/z values and need to feed them to a neural network (e.g., Siamese network for similarity prediction) that requires fixed-size vector input.
    0 installs
79. ▌
    Tof Ms Signal Enhancement Low Abundance 3 · holobiomicslab

    Use when your raw TOF-MS data (Agilent MassHunter .d format) exhibits jagged, artifact-prone peaks in low-abundance ions that compromise peak quality assessment or when you need to improve signal-to-noise before ion mobility demultiplexing or peak deconvolution.
    0 installs
80. ▌
    Mass Spectrometry Tolerance Window Calibration 2 · holobiomicslab

    Use when after feature extraction from raw LC-MS or GC-MS data (using XCMS, MS-Dial, or similar), when you have a feature intensity table with m/z and RT metadata and a reference compound database (known molecules list with m/z, RT, and annotation metadata), and you need to assign confidence-ranked.
    0 installs
81. ▌
    Ms2 Spectrum Extraction And Consensus Building 2 · holobiomicslab

    Use when when you have DDA LC-MS/MS data (mzML format) with identified chromatographic peaks at a specific m/z (e.g., 304.1131) and multiple MS2 spectra fragmented from that precursor, and you need to produce a single high-confidence MS2 spectrum for comparison against reference databases (e.
    0 installs
82. ▌
    Word2vec Model Inference Unknown Word Handling 3 · holobiomicslab

    Use when when applying a pre-trained Word2Vec model to mass spectra at inference time (e.g., library matching or molecular networking), especially when the query spectra may contain fragment peaks or neutral losses not represented in the model's training vocabulary.
    0 installs
83. ▌
    Chemical Annotation Confidence Assessment 3 · holobiomicslab

    Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical explorer visualization, sample filtering, or comparative metabolomics).
    0 installs
84. ▌
    Mass Spectrometry Workflow Orchestration Snakemake 2 · holobiomicslab

    Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
    0 installs
85. ▌
    Peak Boundary Identification In Extracted Ion Data 2 · holobiomicslab

    Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
    0 installs
86. ▌
    Dimension Scale Linking And Cross Group Indexing 3 · holobiomicslab

    Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity data (feature-by-pixel matrix) and metadata groups (featureData, pixelData).
    0 installs
87. ▌
    Multidimensional Feature Detection And Alignment 2 · holobiomicslab

    Use when when you have acquired LC-IMS-MS/MS data (mzML or mzML.gz format) from multiple samples and need to detect features that exploit simultaneous separation in m/z, drift time, and retention time to improve detection sensitivity and reduce false positives.
    0 installs
88. ▌
    Command Line Interface Configuration And Automation 2 · holobiomicslab

    Use when you have a batch of raw LC-IMS-MS/MS data in mzML or mzML.
    0 installs
89. ▌
    Drift Time Retention Time Distance Metric Selection 2 · holobiomicslab

    Use when after peak detection in GCIMS when you need to group detected peaks across multiple samples into reproducible clusters.
    0 installs
90. ▌
    Missing Value Imputation In Quantification Tables 2 · holobiomicslab

    Use when after feature alignment across multiple LC-MS/MS runs, when the unified feature list contains zeros or nulls for specific feature–sample pairs because peaks were not detected in those individual runs, but the feature was detected in other samples in the cohort.
    0 installs
91. ▌
    Tandem Mass Spectrometry Mirror Plot Construction 2 · holobiomicslab

    Use when when you have raw LC-MS or LC-IMS-MS data in instrument format (Agilent .d, Thermo .raw, Bruker .
    0 installs
92. ▌
    Parameter Range Filtering For Chromatographic Data 2 · holobiomicslab

    Use when you have raw MS data in instrument-native or mzML format (Agilent .d, Thermo .raw, Bruker .d) and need to isolate specific analyte regions defined by precise m/z windows, RT windows (in seconds or minutes), and/or ion mobility arrival-time windows.
    0 installs
93. ▌
    Chemical Name Normalization And Publish Database Integra 2 · holobiomicslab

    Use when after spreadOut() has converted raw CSV peak data into a structured list, when you have one or more Compound.Name entries from GC-MS that may be ambiguous, non-canonical, or missing standardized properties (exact mass, published retention times, reactive groups, database presence).
    0 installs
94. ▌
    Ppb Level Marker Detection And Sensitivity Assessment 3 · holobiomicslab

    Use when you have raw GC–MS or LC–MS data in two-dimensional m/z vs retention time format and need to identify marker features at parts-per-billion sensitivity without relying on conventional peak picking.
    0 installs
95. ▌
    Tandem Mass Spectrum Deconvolution Isotope Annotation 2 · holobiomicslab

    Use when you have aligned features characterized across multiple dimensions (m/z, drift time, retention time) and need to: (1) resolve MS/MS spectra that may contain fragments from multiple co-eluting or co-mobilizing precursors; (2) identify and validate isotopic signatures (e.
    0 installs
96. ▌
    Chromatographic Peak Extraction And Retention Time Filte 2 · holobiomicslab

    Use when when you have LC-MS/MS raw data (mzML or netCDF format) and need to isolate a specific compound's signal based on its known or suspected m/z value and retention time range.
    0 installs
97. ▌
    Mz Retention Time Tolerance Parameter Configuration 2 · holobiomicslab

    Use when when invoking Asari to process centroid mzML files for the first time in a PCPFM experiment, or when RT and m/z accuracy characteristics of your LC-MS instrument differ from the pipeline defaults (e.
    0 installs
98. ▌
    Molecular Geometry Neural Network Potential Evaluation 3 · holobiomicslab

    Use when after RDKit has generated multiple conformations for a molecule in an SDF or XYZ format, and you need to reduce the conformational ensemble to a tractable size (by energy-based ranking) before submitting to expensive quantum-chemical calculations (e.g., QUICK).
    0 installs
99. ▌
    Quality Metric Computation From Mass Spectrometry Data 2 · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, or .wiff format) from timsTOF, TripleTOF, or Orbitrap instruments and need to assess their quality before downstream proteomics analysis.
    0 installs
100. ▌
     Search Result Integration With Raw Mass Spectrometry Dat 2 · holobiomicslab

     Use when when you have completed a DIA-MS proteomics search (e.
     0 installs