Use when you have paired metabolomics data (MS/MS spectra and feature quantification) linked to organismal or tissue taxonomy, and you want to reduce false positive annotations…
Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format) and need to identify structurally related metabolites — from…
Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for…
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…
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…
Use when processing SWATH-MS (Sequential Windowed Acquisition of all Theoretical Mass-spectra) raw data files (mzML or vendor format) for untargeted metabolomics, specifically…
Use when when you need to reconstruct or validate the control-flow architecture of a spectral search system that must handle both exact-match library lookups and analogue…
Use when you have a peak intensity matrix from LC/GC-MS analysis with known QC sample indices and suspect batch-related systematic variation in feature intensities.
Use when you have raw or unstructured MS2 spectral data (from untargeted tandem mass spectrometry experiments) and plan to run MS2MP inference for KEGG pathway prediction.
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…
Use when you have high-dimensional replicate experiment data (metabolomics, proteomics, or genomics) with multiple biological or technical replicates per sample, and you need to…
Use when you have raw LC-MS/MS data in mzML or mzXML format and need to: (1) identify the top-abundance MS1 signals in an LC run, (2) compute a single scalar metric (separation…
Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z…
Use when when setting up imzML Writer for the first time on a new machine, or when raw vendor mass spectrometry file conversion fails with ''msconvert not found'' or Docker image…
Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct…
Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or…
Use when when you have trained a regression model on experimental retention times or similar continuous molecular property predictions and need to quantify its generalization…
Use when you have a bioinformatics pipeline (like HiC-Pro) with mixed Python, R, and compiled tool dependencies, and you need to ensure consistent reproducibility across machines…
Use when you have paired in silico and experimental measurements from multiple biological samples (e.
Use when you have sequential QCpool (pooled quality control) samples analyzed with Sciex Multiquant (≥v3.0.
Use when when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to identify and annotate lipid A structures at scale.
Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you…
Use when when you have real LC-MS/MS data (mzML format) from an untargeted metabolomics experiment and want to test how variations in TopN DDA parameters affect which precursor…
Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
Use when after constructing a peak properties dictionary via csv_to_peak_properties
Use when when implementing or refactoring a FileInterface._open method or similar polymorphic dispatcher that conditionally instantiates different handler classes based on file…
Use when you have an unknown mass spectrometry spectrum (acquired experimentally
Use when you have a query mass spectrum matched to multiple candidate metabolites (by accurate mass, database lookup, or spectral similarity), and you possess or can train a DNN…
Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment.
Use when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow…
Use when you are deploying a Windows .NET application (e.g., AirdPro CLI) inside a Docker container on a non-Windows host and need to understand whether Wine initialization…
Use when when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or…
Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce…
Use when you have CE-MS raw data in OnDiskMSnExp format with both positive and negative polarity acquisitions, migration times that vary due to electroosmotic flow drift, and…
Use when when you have an ArchR project object with processed single-cell ATAC-seq data and want to infer developmental or cell-state trajectories.
Use when analyzing differential methylation from bisulfite sequencing data where you suspect overdispersion (variance exceeds binomial expectations), or when comparing uncorrected…
Use when when you have high-resolution LC-MS/MS data for an unknown metabolite or small molecule, have computed or measured the molecular ion mass and fragmentation spectrum, and…
Use when when you have received Sciex Multiquant TXT export files from a completed metabolomics or lipidomics analytical run and need to verify that QC pool samples were injected…
Use when you need to run the Zamboni-lab Masster (MASSter) workflow for untargeted LC-MS metabolomics data analysis.
Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical…
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…
Use when you have 512-dimensional representation vectors output from paired ResNet18 encoders processing augmented ion images, and you need to: (1) introduce an intermediate…
Use when when exporting in-memory generated spectra as MSP-format spectral libraries, you must first map each spectrum record to required MSP fields (NAME, PRECURSORMZ, SPECTRUM)…
Use when an ASB skill proved wrong, stale, missing or wasteful in practice — its steps failed, no skill covered the task, the leaves existed but nothing composed them, or the tool…
Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that may contain multiple MS2 spectra per feature and require reduction or standardization before library matching.
Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredic — from…
Use when after running annotateRC on LC–MS AIF data when you need to inspect whether a feature has multiple plausible annotations (e.g., isobaric lipids, isomers with the same…
Use when you have a labeled peak quality dataset (development set with ground-truth pass/fail labels), a defined set of peak-quality metrics (e.
Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.
Use when apply peak-count capping when preprocessing tandem mass spectrometry (MS/MS) spectra for peptide identification or spectral library matching, particularly when working…
Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform…
Use when when you have applied biotransformation rules to generate candidate product structures from a set of input molecules (represented as SMILES strings) and need to document…
Use when immediately after calling squidpy.gr.spatial_neighbors() or similar spatial graph construction methods on an AnnData object.
Use when you have two implementations of the same quantification method (or major versions) and observe a persistent disagreement in mapped-read counts, per-read alignment…
Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm…
Use when after peak picking by MS-DIAL and import into R, when the feature table contains m/z values with decimal components that fall within the [4, 8] interval (indicating…
Use when after structural cluster assignment and correlation clustering are complete, and you need to represent the full set of structural relationships (isotopologues, adducts,…
Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or…
Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
Use when you have a SummarizedExperiment object containing pooled quality control samples with measured compound and internal standard peak areas.