Coding & Dev Tools

holobiomicslab Skill

Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request. The skill is essential before pushing feature branches to the repository or merging changes into master.

holobiomicslab Skill

Use when after removing precursor and noise peaks from an MsmsSpectrum object when the spectrum contains peaks with highly variable intensities (e.g., one or two dominant peaks with many weaker fragments).

holobiomicslab Skill

Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that spectrum to the appropriate domain-specific MASST application for searching.

holobiomicslab Skill

Use when after applying CordBat batch correction to a log2-transformed metabolite matrix from multi-batch metabolomics data, you want to quantitatively and visually assess whether the correction successfully reduced batch effects.

holobiomicslab Skill

Use when you have computation-time metrics from a gallery or benchmark suite comparing multiple plotting backends on the same data types (e.

holobiomicslab Skill

Use when after feature extraction from mzML/mzXML files when you have identified candidate peaks in breath spectrometry data but need to separate true VOC signals from instrument noise.

holobiomicslab Skill

Use when when you have a list of lipids identified by different database identifiers (e.

holobiomicslab Skill

Use when apply log-transformation immediately after loading a raw metabolomics featuredata matrix (metabolite peak intensities as rows=samples, columns=metabolites) and before normalization.

holobiomicslab Skill

Use when when you have pre-processed genomic data (GCFs from AntiSMASH/BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to systematically score and rank putative relationships between biosynthetic gene clusters and their.

holobiomicslab Skill

Use when you have an annotated or raw tandem mass spectrometry spectrum and need to identify which observed peaks correspond to expected peptide fragment ions from a known or predicted peptidoform. Use it before spectrum visualization if you want highlighted, labeled fragment matches;

holobiomicslab Skill

Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks correspond to expected b-ion and y-ion fragments, in order to validate peptide identification or annotate spectrum quality.

holobiomicslab Skill

Use when you have a collection of MS/MS spectra from reference standards representing your compounds of interest (e.g., flavonoids, prenylated chalcones) and a set of MS/MS spectra from non-target or other compounds.

holobiomicslab Skill

Use when you have experimental mass spectrometry spectra (LC–QTOF or similar format) from unknown compounds and need to predict their molecular structures.

holobiomicslab Skill

Use when you have acquired .raw files from a Thermo mass spectrometer (e.g., Q Exactive, Orbitrap) and need to expose their contents—scan numbers, retention times, m/z values, intensities, and precursor information—for downstream nontargeted LCMS feature detection and alignment.

holobiomicslab Skill

Use when when implementing or auditing S4 replacement methods (e.

holobiomicslab Skill

Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to label experimental features by biomolecular class before performing CCS calibration or validation.

holobiomicslab Skill

Use when when you have a collection of molecular structures (SMILES or SDF format) and need to generate a queryable database of collision cross section values for high-throughput mass spectrometry workflows, or when you want to organize pre-computed CCS predictions with conformer metadata into a.

holobiomicslab Skill

Use when when implementing an igzip parser, decoder, or validator that must interpret the custom header format; when debugging igzip file corruption or encoding errors; or when extending pymzML's igzip support to handle new index schemes.

holobiomicslab Skill

Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have been attenuated without loss of data dimensionality or sample information.

holobiomicslab Skill

Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or databases).

holobiomicslab Skill

Use when you have peak-picked features with m/z, drift_time, retention_time, and intensity columns, and you need to identify monoisotopic peaks and their charge-state-specific isotopologue members (e.g., singly charged C13-substituted species).

holobiomicslab Skill

Use when when implementing fragment ion annotation in proteomics workflows and needing to determine whether neutral loss annotation (e.g., H2O: -18.010565, NH3: -17.026549) should be enabled to maximize peak interpretation.

holobiomicslab Skill

Use when when you need to assess whether retention times measured on a given LC-MS run follow the expected linear relationship defined by iRT peptide standards (e.g., Pierce or Biognosys iRT peptides).

holobiomicslab Skill

Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and intensity pairs), and you seek to generate candidate molecular structures for an unknown metabolite that may not be in.

holobiomicslab Skill

Use when after running the annotateRC function on LC-MS All-ion fragmentation (AIF) features and obtaining a populated annotations object with ranked candidate matches, use this skill when you need to persist results to disk for archival, sharing, or downstream interpretation (e.

holobiomicslab Skill

Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic signatures to distinguish monoisotopic peaks from isotopologues, reduce feature redundancy, and support multi-dimensional.

holobiomicslab Skill

Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.

holobiomicslab Skill

Use when when implementing or modifying data replacement methods (e.g., `mz<-`, `peaksData<-`) in a writable MsBackend subclass, or when accepting user-supplied m/z vectors destined for storage in a Spectra backend.

holobiomicslab Skill

Use when after LDA modeling has produced an inferred motifset (JSON format) containing Mass2Motifs with fragment and neutral-loss patterns.

holobiomicslab Skill

Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend. Triggers include: (1) implementing a replacement method (e.g., mz<- or intensity<-) for a backend class;

holobiomicslab Skill

Use when you have mass spectrometry raw data in mzML format (including compressed variants like mzML.

holobiomicslab Skill

Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax or mzapy.peaks.find_peaks_1d_gauss) on synthetic mass spectra with known peak locations and heights.

holobiomicslab Skill

Use when when you need to verify or retrieve package-internal metadata about compiled .NET assembly location and version before processing raw mass spectrometry files, or when testing the R↔C# dispatch mechanism in isolation without loading actual Orbitrap .raw data files.

holobiomicslab Skill

Use when when you have mzPeak format spectrum files and need to work with spectrum metadata, intensity/m/z arrays, or precursor information in a tabular, columnar, or vectorized computing environment.

holobiomicslab Skill

Use when working with raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d format) prior to noise thresholding and mass-domain calibration.

holobiomicslab Skill

Use when when rendering spectrum data (m/z vs. intensity arrays) from MZA files and need to control visual presentation: applying m/z range windows, setting line colors and labels for legend identification, sizing the figure, or choosing between interactive display versus file export.