Coding & Dev Tools

holobiomicslab Skill

Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a reference library.

holobiomicslab Skill

Use when when you need to quantify and compare the effect of multiple filtering thresholds (e.g., Match.Factor ≥65, ≥80, ≥90) on the size of a retained compound set.

holobiomicslab Skill

Use when you have a mass spectrum scan containing observed precursor ions (m/z, intensity pairs) in a narrow isolation window, a known peptide sequence with specified charge state and stable isotope labeling parameters (atom type, incorporation probability), and you need to determine which observed.

holobiomicslab Skill

Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the search must be executed against the appropriate domain-curated spectral library.

holobiomicslab Skill

Use when you have raw MS imaging data in imzML (continuous or processed) or Analyze 7.5 format and need to load it into R for spectral processing, normalization, peak-picking, or statistical analysis.

holobiomicslab Skill

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.

holobiomicslab Skill

Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula and connectivity) rapidly without access to 2D NMR experiments (HSQC, HMBC, COSY) or mass spectrometry.

holobiomicslab Skill

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.

holobiomicslab Skill

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..

holobiomicslab Skill

Use when you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.

holobiomicslab Skill

Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a selected noise-filtering strategy retains an expected number of peaks for downstream molecular formula assignment.

holobiomicslab Skill

Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and wish to identify peptidic natural products or ribosomally synthesized and post-translationally modified peptides (RiPPs) against a known structure database or custom RiPP structure database.

holobiomicslab Skill

Use when when ingesting raw LC-MS/MS output from a mass spectrometry instrument and you need to prepare it for metabolite identification, fragmentation tree computation, or molecular formula annotation.

holobiomicslab Skill

Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes molecules by chemical taxonomy.

holobiomicslab Skill

Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA-MS data) and need to identify precise peak boundaries and apex positions for feature extraction.

holobiomicslab Skill

Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing pipelines.

holobiomicslab Skill

Use when after applying one or more intensity drift correction strategies (Internal Standard correction, statistical drift correction, custom or weighted bracketing) within QuantyFey and before exporting the corrected intensity table for final quantification.

holobiomicslab Skill

Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.

holobiomicslab Skill

Use when you have MS/MS spectra (centroided m/z and intensity pairs) and corresponding MS1 precursor masses but lack reference spectra or a priori formula information.

holobiomicslab Skill

Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.

holobiomicslab Skill

Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct a molecular network.

holobiomicslab Skill

Use when when you have 1D NMR spectra (¹H and/or ¹³C) as input and need to predict complete molecular structure (both molecular formula and bond connectivity) for molecules with up to 19 heavy atoms.

holobiomicslab Skill

Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .

holobiomicslab Skill

Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative identifications).

holobiomicslab Skill

Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification, and you need to identify which observed peaks correspond to specific fragment ion types (e.g., only b and y ions for backbone fragmentation, or immonium ions for amino acid identification).

holobiomicslab Skill

Use when you have candidate lipid annotations from spectral library matching (e.g., XCMS + CAMERA output) with MS/MS scores, and you need to reduce false positives and predict previously unannotated lipids.

holobiomicslab Skill

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

holobiomicslab Skill

Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer in its native export format and need to ingest it into LipidMatch for lipid identification.

holobiomicslab Skill

Use when you need to store or retrieve mass spectrometry spectra (m/z and intensity pairs) from a novel data source or storage medium (e.

holobiomicslab Skill

Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural annotations (missing SMILES or molecular formula fields) and need to combine them into unified, polarity-specific msp files.

holobiomicslab Skill

Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified peptides (RiPPs) by integrating genomic and mass spectrometry data.

holobiomicslab Skill

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

holobiomicslab Skill

Use when setting up a Rapid QC-MS monitoring job and you need to define WHERE and HOW QC-fail alerts should be sent.

holobiomicslab Skill

Use when when constructing a comprehensive lipid spectral reference library that must disambiguate lipids differing only in carbon-carbon double-bond position (e.

holobiomicslab Skill

Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing. Specifically, when you must extract precursor m/z values, peak intensity pairs, and spectrum metadata (e.

holobiomicslab Skill

Use when after batch correction of metabolomics QC samples using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to determine which one stabilizes the compound/internal standard ratio for each compound.