Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is…
Use when you have a compiled EI or MS2 library object (read from MSP format via read_lib) and access to NIST ri.dat and USER.DBU files; you need to populate RI values for…
Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to…
Use when you have LC-HRMS profile-mode chromatograms with extracted local maxima exported as standardized 2D rt×mz areas, and you need to disambiguate true chromatographic peaks…
Use when when searching for peptide spectra with unknown or open modifications (i.e., any mass shift within a broad tolerance range rather than a fixed set of known modifications).
Use when when you have mass spectrometry ion image data and need to learn meaningful low-dimensional representations through self-supervised contrastive learning.
Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by…
Use when training embeddings from multi-modal spectral data (peak information + metadata) where you need to ensure both contrastive discriminability AND reconstruction fidelity.
Use when when you have a neural network or machine learning model with multiple tunable hyperparameters (layer size, regularization strength, dropout) or design choices (e.
Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score…
Use when when you have execution time data for visualization scripts across multiple backends (matplotlib, Bokeh, Plotly) and need to determine which backend offers the fastest…
Use when after database search algorithms have scored unknown MS samples against reference species, and you need to visually inspect and confirm species assignments or identify…
Use when you have a filtered set of non-overlapping peaks from ATAC-seq data and a collection of motifs (typically from JASPAR or similar databases), and you need to identify…
Use when you have a fitted linear model (lmFit object) from microarray, RNA-seq, qPCR, or proteomics data and need to test for differential expression across genes while…
Use when you have assembled genome sequences (contigs or scaffolds in FASTA format) and want to identify putative BGCs and their precursor peptides before constructing a RiPP…
Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time…
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…
Use when you have a GC-MS dataset with a Match.Factor column (output from Agilent Unknowns Analysis or equivalent) and need to retain only high-confidence compound identifications.
Use when you have paired mass spectra and molecular structure datasets and need to train a model that jointly understands both modalities for tasks like structure elucidation.
Use when you have a published research article describing a new FT-ICR MS analysis tool and need to verify which analytical and visualization features are actually implemented…
Use when you have long-read RNA-seq samples quantified by oarfish (output as quant.gz files) and need to extract transcript-level or gene-level abundance, count, and length…
Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.
Use when your input is a tabular file (CSV or Excel) with column headers annotated using MESSES tagging syntax (#<table_name>.id for record identifiers and #.
Use when you have a published predictive model with known coefficients and feature requirements (e.g., MetaboAge from a peer-reviewed study), a target R package with an…
Use when when you need to construct a dual-branch neural network encoder that processes two augmented versions of the same input (e.g., ion images in COL or ISO mode) and must…
Use when when implementing or auditing a deep learning pipeline for MS/MS-based molecular formula prediction, verify that precursor m/z values in the input feature array are…
Use when when you have raw MS/MS spectra in MGF or mzML/mzXML formats and need to feed them into Casanovo or similar transformer-based de novo sequencing models.
Use when you have a collection of molecular fingerprint vectors (such as biosynfoni count fingerprints) and need to measure structural similarity between all pairs of molecules.
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 beginning an untargeted LC-MS analysis and either (1) the dataset characteristics (sample complexity, instrument platform, or polarity) differ from previously…
Use when you have a generic genome-scale metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, extracellular flux measurements from…
Use when when you have an observed MS/MS spectrum and need to annotate fragment peaks against a known modified peptide sequence.
Use when before initiating raw file conversion or feature extraction, when you have a heterogeneous collection of raw LC-MS files (.raw or .mzML) and sample information scattered…
Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly…
Use when when you have a collection of DNA adduct compound structures in SDF format that requires validation for structural integrity and completeness, and you need to generate…
Use when when you have chemical annotations (GNPS matches) distributed across multiple sample groups (e.g., by sample type, extraction method, ionization source) with unequal…
Use when when you have imported a raw GCxGC-MS chromatogram as a 2D-TIC (2D Total Intensity Chromatogram) object from a NetCDF file and observe steady or increasing baseline…
Use when when you have metabolomics results from multiple studies reporting compound identifiers, p-values, fold-changes, and study sizes (N), and you need to prepare them for…
Use when after extracting and encoding molecular descriptors and structural features (atom types, bond connectivity, graph topology) from SMILES strings into a fixed-size…
Use when after peak annotation when you have: (1) a peak intensity matrix (rows=peaks with KEGG/ChEBI/UniProt IDs, columns=samples) with group labels; (2) a pathway database…
Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.
Use when after extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument…
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…
Use when you have a trained shallow decision tree on ChemEcho feature vectors (sparse, high-dimensional representations of tandem mass spectra peaks and neutral losses) and need…
Use when you have untargeted MS2 spectral data in MS2MP-compatible format and need to assign KEGG pathway annotations to spectra without spectral library matching or manual…
Use when after calculating 12 peak-quality metrics on a development set of extracted ion chromatograms (EICs) and labeled peaks, when you need to select both the classification…
Use when when processing LC-MS metabolomics datasets with 10 or fewer samples and requiring reproducible mass track alignment across the cohort.
Use when when deploying a multi-service microarchitecture (such as MAGMa''s four distinct subprojects: magmaweb, joblauncher, job, and pubchem) via Docker Compose and you need to…
Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains…
Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the…
Use when you have pre-processed chromatin accessibility data (ATAC-seq or DNAse-seq) with chromVAR deviations already computed for individual cells or bulk samples across multiple…
Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and…
Use when processing heterogeneous mass spectral datasets from multiple open libraries (e.g., MassBank, UNPD, GMD) where structural identifiers, precursor m/z, and adduct…
Use when you have a Thermo Fisher Scientific .raw file from an LC-MS run containing a spiked iRT peptide standard mix (e.
Use when you have a peak list extracted from MSI data that includes candidate peaks with potential m/z overlap or spatial co-localization patterns across tissue images.
Use when apply TMM normalization when you have raw RNA-seq read counts from multiple samples and suspect differences in library composition (e.g., one sample over-represents a…
Use when when you have preprocessed 1H NMR spectral data with unidentified peaks and need to determine metabolite identity by exploiting the correlation structure of NMR signals.
Use when you need to run the Zamboni-lab Masster (MASSter) workflow for untargeted LC-MS metabolomics data analysis.
Use when you have a normalized gene expression matrix (genes × samples) and an experimental design with known treatment groups or conditions, and you need to estimate the effect…
Use when training a contrastive encoder on mass spectrometry imaging (MSI) data in ISO mode (isotope ions from the same molecule).