Coding & Dev Tools

holobiomicslab Skill

Use when you have a quantification table (rows = metabolite features, columns = samples with abundance values), corresponding metadata table (sample annotations, groupings), and spectral data files, and you need to produce a unified JSON dashboard artifact that can be loaded into an interactive.

holobiomicslab Skill

Use when you have run MSMetaEnhancer's annotate_spectra() method on a .

holobiomicslab Skill

Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization features are already implemented in competing or complementary tools (e.

holobiomicslab Skill

Use when you have uploaded peak list data containing m/z values and wish to construct a Kendrick mass plot where alkane homolog series (or other homologous families) are expected to appear as horizontal lines.

holobiomicslab Skill

Use when your metabolomics experiment includes samples acquired across multiple instrument runs, different preparation dates, or distinct sample cohorts.

holobiomicslab Skill

Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise distance computation is computationally prohibitive.

holobiomicslab Skill

Use when you have DDA raw mass spectrometry data (mzML, mzXML, or netCDF format) and need to reconstruct composite fragmentation spectra by associating fragment ions with their parent precursor ions.

holobiomicslab Skill

Use when after structural cluster assignment and correlation clustering are complete, and you need to represent the full set of structural relationships (isotopologues, adducts, cross-assay links, and correlation co-membership) in a single unified graph for interactive visualization, network.

holobiomicslab Skill

Use when you have raw or curated mass spectrometry data (MS1, MS2, or MSMS) in mzML, mzXML, CDF, MGF, MSP formats, or from a MassBank/MetaboLights repository, and need to convert it into an in-memory or on-disk spectral object that supports filtering, comparison, and annotation workflows.

holobiomicslab Skill

Use when you have a mass spectrometry visualization library that claims to support multiple plotting backends and need to verify that: (1) all backends produce functionally equivalent outputs, (2) execution times are consistent with reported benchmarks, and (3) the library scales appropriately.

holobiomicslab Skill

Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that depends on specific versions of auxiliary packages (like spectrum-utils==0.3.5).

holobiomicslab Skill

Use when after aligning fragment ions between two tandem mass spectra (query and reference) using maximum weight matching and you need to assign confidence scores to the matched ion pairs.

holobiomicslab Skill

Use when you have uploaded a delimited data file (comma-, semicolon-, or tab-separated) with a header row into Punc'data and need to ensure that each column is correctly mapped to its semantic role (m/z, intensity, formula, or other mass spectrometry attributes) before proceeding to analysis.

holobiomicslab Skill

Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links using metabolite structure information rather than genomic or strain-based features alone.

holobiomicslab Skill

Use when you have multiple high-resolution mzML files from LC-MS/MS experiments (e.

holobiomicslab Skill

Use when after feature detection and quality control have produced a feature table in TSV format from Asari or equivalent preprocessing.

holobiomicslab Skill

Use when when you have preprocessed MALDI-MSI data (in msimat format) and want to determine whether abundant peaks are actually molecular adducts of simpler parent ions rather than distinct metabolites.

holobiomicslab Skill

Use when you have centroided data-dependent acquisition (DDA) mzML files from LC- or GC-HRMS measurements and need to convert continuous raw mass spectrometric signals into discrete, quantifiable chromatographic features (m/z, RT, intensity, charge, isotope) before PFAS-specific prioritization or.

holobiomicslab Skill

Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the software performs in silico generation, enumeration, or filtering of candidate molecular structures and the published paper or.

holobiomicslab Skill

Use when you have a spectral library with structural ground truth (InChIKey or SMILES annotations for ≥50% of spectra) and want to benchmark whether a new or existing spectral similarity scorer ranks structurally related compounds higher than unrelated ones.

holobiomicslab Skill

Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.

holobiomicslab Skill

Use when when you have received metabolomics mass-spectrometry data in vendor-native or open formats (.raw, .d, mzXML) and need to ingest it into SMART for preprocessing, peak detection, or statistical analysis.

holobiomicslab Skill

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.

holobiomicslab Skill

Use when when you have preprocessed non-targeted LC-MS/MS feature tables (post-merging, cleanup, blank removal, and batch correction) and seek to uncover multivariate patterns across samples, discriminate between experimental groups, or reduce dimensionality of high-dimensional metabolomic data.

holobiomicslab Skill

Use when when you have loaded mass spectrometry data (from mzML or Bruker .

holobiomicslab Skill

Use when you have LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and corresponding genomic sequence data (raw FASTA nucleotide sequences or genome mining tool outputs like antiSMASH .final.

holobiomicslab Skill

Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and perform structured chemical similarity analysis.

holobiomicslab Skill

Use when you have MS/MS spectra with fragment frequency annotations (from consensus spectrum generation) and need to decide which fragments to retain versus remove. Trigger conditions: (1) you have replicate MS/MS spectra for the same feature with per-fragment recurrence frequencies calculated;

holobiomicslab Skill

Use when mS quantification data exhibits intensity drift—a systematic decline or variation in detector response across the run sequence. Intensity drift is particularly common in long measurement sessions and compromises the accuracy of feature-by-sample intensity matrices.

holobiomicslab Skill

Use when you have metabolomics metadata in mwTab or tabular format with column headers and values that may contain database identifiers (e.g., HMDB IDs, PubChem CIDs, KEGG compound IDs) in heterogeneous or non-canonical formats (mixed case, optional prefixes, variable naming conventions).

holobiomicslab Skill

Use when after MS1 feature detection and accurate mass annotation, when you have identified a set of blank injections (negative controls) run in the same analytical sequence segment as your biological or study samples.

holobiomicslab Skill

Use when when deploying containerized versions of a multi-variant application (e.g., CLI, development, Linux, and Windows flavors) and you need to verify that each built image meets documented size constraints before registry push or production release.

holobiomicslab Skill

Use when when performing feature detection on centroided DDA mzML files from LC- or GC-HRMS and you need to confirm the elemental composition or differentiate between candidate features—particularly for PFAS screening where isotopic signatures (chlorine, bromine, fluorine) are diagnostic.