Use when you have raw GC-MS output exported as CSV (containing columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.
Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to…
Use when you have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and…
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…
Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed…
Use when you have raw mass spectrometry files in standard formats (mzML, mzXML, msp, MGF, JSON) and need to extract precursor m/z values, fragment peaks, neutral losses, retention…
Use when you have raw mass spectra or processed feature matrices from liquid chromatography–mass spectrometry (LC-MS) or direct infusion MS that must be ingested by a deep…
Use when you have raw mass spectrometry outputs (peak areas/heights across samples and fragmentation spectra) that need to be formatted and validated before running the tima…
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.
Use when you have received an mzPeak archive (a ZIP file containing Parquet tables) and need to understand its internal structure, validate that spectrum metadata aligns with…
Use when after feature extraction and peak recognition have produced detected MS/MS spectra (precursor m/z, charge, retention time, and fragment ion peaks), and you need to export…
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 after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or…
Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV) loaded into a Pandas DataFrame with columns for m/z, retention time, ion mobility, or intensity values, and…
Use when you have an unknown mass spectrum (or a representative metabolite spectrum from public data) and need to identify it by comparing it against a large reference…
Use when when you have raw ion mobility-mass spectrometry data (drift times, m/z values, and frame metadata) from DTIMS-MS, TWIMS-MS, or SLIM-based instruments and need to compute…
Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert individual spectra into fixed-dimensional vector — from…
Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized…
Use when you have uploaded MS/MS data to MassIVE with validated sample-information
Use when after MSConvert has converted vendor-specific raw mass spectrometry data (ThermoFisher, Agilent, or equivalent formats) on a Linux system and before initiating analysis…
Use when you have mzML or mzXML mass spectrometry data files and need to extract and validate spectral records (m/z and intensity arrays) for lossless compression, lossy…
Use when when preparing raw mass spectrometry imaging (MSI) ion images for deep learning–based representation learning, especially when you need to generate augmented image pairs…
Use when you have raw or preprocessed MS imaging data archived as an RDS file or from a Zenodo deposit that includes the full m/z feature set (e.g., 10,200 m/z values spanning…
Use when you have raw mass spectrometry imaging data (2D or 3D spatial coordinates with full mass-to-charge spectra) and want to train a probabilistic deep learning classifier for…
Use when you have raw mass spectrometry data from an instrument not yet validated in your pipeline (e.
Use when when you have a feature table from LC-MS preprocessed data (e.g. from asari v1.9.2) and need to annotate ions and infer neutral mass.
Use when when preprocessing a public MS/MS spectral library (e.g., GNPS) for machine learning and you discover discrepancies between expected and observed compound counts after…
Use when when you have an unknown MS/MS spectrum (with ≥10 peaks, precursor m/z, and at least 5 fragment ions) and need to identify it by comparing against a curated spectral…
Use when when you have an unknown MSMS spectrum (precursor m/z and fragment ions) and need to discover structurally related compounds from a spectral library.
Use when when you have detected peaks in a direct injection FTICR-MS mzML file (or similar high-resolution MS format) and need to assess whether m/z measurements are accurate and…
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 when you need to create negative control or background-only reference datasets for LC/GC-MS analysis pipelines—specifically to validate peak-picking algorithms, assess…
Use when when integrating LC-MS/MS data from diverse sources (e.g., public repositories like MSV000080102, instrument outputs, or precomputed workflows) into NPDtools pipelines.
Use when you have a Thermo Fisher Orbitrap .raw file and need to programmatically
Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or…
Use when when you have a Thermo Fisher Scientific Orbitrap .raw file and need to confirm that a targeted acquisition method (e.g., PRM targeting a specific precursor m/z) is…
Use when when you have raw mass spectrometry data from direct-infusion (DI-MS) or ambient surface analysis probe (ASAP-MS) instruments and need to identify which m/z peaks are…
Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity…
Use when you are building a visualization library that must support multiple plot kinds (chromatogram, spectrum, mobilogram, peakmap) across multiple rendering backends…
Use when when processing centroided .mzML LC–MS runs with a multi-polarity target list (i.e., some targets ionize in positive mode, others in negative mode, or both) and you need…
Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate…
Use when when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) that must be fed into a CNN model for metabolite annotation…
Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).
Use when when you need to enable users to express complex mass spectrometry search patterns (e.
Use when you have positive- or negative-mode tunemix reference data (with known CCS values, m/z, and measured drift times) and need to establish a calibration model for converting…
Use when you have acquired tunemix data (positive or negative ion mode, in .h5 format) with known CCS reference values and need to construct a calibration function that will later…
Use when you have raw LC-MS/MS chromatogram files in mzML/mzXML format (converted from Thermo, Waters, or Bruker instruments) acquired in DDA or targeted MS/MS mode, and you need…
Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs.
Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally modified variant of that compound—and you need to identify which atoms in — from…
Use when you have raw mass spectrometry spectra from an unknown analyte or a synthetic compound library and need to feed them into PS2MS or similar deep learning classifiers for…
Use when you have pre-processed MS/MS spectra and need to prepare them for word-embedding-based similarity methods (e.g., Spec2Vec).
Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
质谱分析工具 skill。用于 PyOpenMS、OpenMS、matchms、mzML/mzXML、feature detection、RT alignment、spectral similarity、peptide/protein identification、metabolite annotation 和 MS 数据结构处理。
Use when when you have raw mass spectrometry transition data from a triple-quadrupole
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…
Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
Use when when you have Thermo Fisher Scientific .raw files from Orbitrap instruments and need to build a quantitative summary of MS1 acquisition intensity dynamics across a…
Use when after applying frequency domain calibration (Ledford, linear, or quadratic equation) to a raw FT-ICR mass spectrum, validate the calibration quality by measuring residual…
Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your…