Next Gen Web Apps
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Apps
Maintained and documented tools, shipped with the repo.
CORS API Tester
Fire live cross-origin requests from your browser at several GNPS2 servers at once — pull an Everything-Bagel task file and MS/MS peaks from the resolver — and see which servers allow this page
FASST Search
The simplest way to run a FASST spectral search: paste a USI or a peak list, pick a database, get matches. Powered by the public api.fasst.gnps2.org.
GNPS2 Networking Packager
Enter a GNPS2 molecular networking task (Classical, FBMN, or Everything Bagel) and package its result files into a .zip with a README describing every file — ready to hand to Claude.
GNPS2 → Cytoscape .cys Generator
Turn a GNPS2 molecular-networking task (or a network.graphml) into a ready-to-open Cytoscape .cys session — nodes, edges, molecular-family groups, and the GNPS pie-chart style — built entirely in your browser.
MassQL Playground
Write a MassQL query, see it explained in plain English, and run it against your own mzML/MGF/JSON file — MassQL running entirely in your browser.
MS/MS Structure Consistency
Check whether a structure (SMILES) is consistent with an MS/MS spectrum and adduct — precursor mass match plus in-silico fragment annotation — all in your browser, shareable by URL or USI.
mzML / mzXML Viewer
Drag-and-drop one or more files to render MS1 heatmaps, overlay TICs, and extract XICs — all in the browser.
PubMed Collaborators
Build the co-author list for an NIH/NSF conflict-of-interest table from PubMed — every co-author in a chosen window, their most recent affiliation and last shared paper — entirely in your browser.
Structure → Mass Calculator
Paste SMILES to get molecular mass, adduct m/z, and isotope peaks, then compare an observed precursor with the structure or a formula in ppm.
In development
Committed to the repo but still a work in progress — usable, but the
interface and results may change. An app opts in with
<meta name="status" content="dev">.
Agilent to mzMLIn dev
Convert Agilent MassHunter .d folders to mzML entirely in your browser. Drop whole .d directories, convert Q-TOF data (profile scans centroided), and download the mzML. Files never leave your machine.
Batch MASST SearchIn dev
Drop an mzML/MGF file or a table of USIs, search every spectrum against all public metabolomics data with fastMASST, and download the compiled hits — spectra are read in your browser, no upload.
Bruker timsTOF to mzMLIn dev
Batch-convert Bruker timsTOF .d acquisitions (TDF / TSF, DDA-PASEF) to mzML entirely in your browser — drop many .d folders, convert in parallel, and stream straight to a folder. Files never leave your machine.
Bruker timsTOF ViewerIn dev
Browse a Bruker timsTOF .d acquisition in your browser — metadata, spectrum navigation, and per-spectrum m/z plots with ion mobility (1/K0), precursor and CCS — powered by a pure-Rust WebAssembly engine. Nothing is uploaded.
CorrOmicsIn dev
Correlate two omics feature tables across shared samples to find associated feature pairs and export a Cytoscape-ready network — entirely in your browser.
FBMN-STATS GuideIn dev
A browser-only statistics workbench for feature-based molecular networking — load a feature table and metadata, then run PCA, PCoA/PERMANOVA, clustering heatmaps and univariate tests. Your data never leaves your machine.
foodMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which foods it was observed in — hits mapped onto the foodMASST reference tree, entirely in your browser.
GNPS2 Error ExplainerIn dev
Paste a GNPS2 error (or a task ID) and get a plain-language explanation and likely fix — powered by the GNPS2 WebAgent LLM, signed in with your GNPS2 account.
MASST SearchIn dev
Search a single MS/MS spectrum (by USI) against all public GNPS/MassIVE data or the GNPS libraries with fastMASST — matches, datasets, and cosine — entirely in your browser.
microbeMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which microbes it was observed in — hits mapped onto the microbeMASST reference tree, entirely in your browser.
microbiomeMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which microbiome sample groups it was observed in — hits mapped onto the microbiomeMASST reference tree, entirely in your browser.
MMSAIn dev
Multiple Mass Spectral Alignment: line up every spectrum in a molecular-networking component and see which peaks are shared across the family — computed entirely in your browser.
ModiFinderIn dev
Localize the site of a chemical modification on a known structure from a pair of MS/MS spectra (known + modified analog) — combinatorial fragmentation and per-atom scoring, all in your browser.
Multi-step MassQLIn dev
Classify bile-acid isomers in a GNPS2 molecular-networking job with a validated multi-step MassQL query sequence — stage-1 filtering, stage-2 confirmation, isomer leaves, and a classification tree — entirely in your browser. A client-side port of the Multi-step MassQL MetaboApp.
personalCareProductMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which personal care products it was observed in — hits mapped onto the personalCareProductMASST reference tree, entirely in your browser.
plantMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which plants it was observed in — hits mapped onto the plantMASST reference tree, entirely in your browser.
PostMN MassQLIn dev
Run MassQL spectral-pattern queries on the consensus MGF of a GNPS2 molecular-networking job — by Task ID or by dropping the MGF — entirely in your browser. A client-side port of the PostMN MassQL MetaboApp.
RAW to mzMLIn dev
Batch-convert Thermo .raw files to mzML entirely in your browser — drop 100 at once, convert in parallel, and download them all. Files never leave your machine.
SpectraCodec DecoderIn dev
Drag in self-describing mzML files (SpectraCodec) and pull the embedded experiment metadata out of the spectra — decoded in parallel across CPU cores in your browser, scaling to hundreds of files, exported as one metadata table.
tissueMASSTIn dev
Search one MS/MS spectrum (by USI) against all public GNPS/MassIVE data with fastMASST, then see which tissues and body sites it was observed in — hits mapped onto the tissueMASST reference tree, entirely in your browser.
TPP SolverIn dev
Thermal Proteome Profiling analysis: sigmoidal melting-curve fitting, melting-point (Tm) shifts, and Mann-Whitney/Benjamini-Hochberg statistics — entirely in your browser, your data never leaves your machine.
Sandbox
Deploy an app →Experiments uploaded through the drag-and-drop deployer. Unreviewed and subject to change or removal at any time.