Pyxis

Your AI Analytical Chemistry Assistant

Upload your existing MS2 data to Pyxis and get automated IDs and relative quantitation in minutes. No additional sample prep or instrument time needed.

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October 2025

Introducing LSM-MS2

We're excited to introduce LSM-MS2-enabled-ID in Pyxis, our first major capability release for MS/MS spectra. LSM-MS2 represents a significant advancement in how researchers identify and interpret metabolites from raw mass spectrometry data. Upload your data, get comprehensive identifications with scores, then analyze with Pyxis' statistical and visualization tools. Available today.

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Import MS2 spectra files directly into the platform

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AI Analysis

Our model identifies biomolecules automatically

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Review Results

Examine scores and identification details

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Create visualizations and export findings

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No parameter tuning. No configuration files. No PhD required.

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Pyxis • Zero Configuration

Drop your file here

Supports mzML, mzXML, and raw files

plasma_samples_2024.mzML

142.3 MB • 2,847 features detected

Analyzing your data...

Usually completes in under 5 minutes

Processing features 0%

What we're doing automatically:

Optimizing mass tolerance parameters

Selecting relevant metabolite databases

Configuring adduct and isotope patterns

Calculating scores

Analysis Complete

1,923 identifications in 4:52

Compound	m/z	Score
L-Glutamine C₅H₁₀N₂O₃	147.0764	98%
Database HMDB HMDB ID HMDB0000641 Adduct [M+H]⁺ RT 2.34 min Spectral Match Score 98% match
L-Phenylalanine C₉H₁₁NO₂	166.0863	96%
Database KEGG KEGG ID C00079 Adduct [M+H]⁺ RT 3.12 min Spectral Match Score 96% match
Creatinine C₄H₇N₃O	114.0662	94%
Database HMDB HMDB ID HMDB0000562 Adduct [M+H]⁺ RT 1.87 min Spectral Match Score 94% match
Tryptophan C₁₁H₁₂N₂O₂	205.0972	87%
Database HMDB HMDB ID HMDB0000929 Adduct [M+H]⁺ RT 4.21 min Spectral Match Score 87% match
Citric acid C₆H₈O₇	193.0348	92%
Database KEGG KEGG ID C00158 Adduct [M+H]⁺ RT 1.54 min Spectral Match Score 92% match

💡 Click any compound to view detailed information

Industry-leading accuracy

Validated against rigorous scientific benchmarks, Pyxis consistently delivers results you can trust for critical research decisions.

Internal Isomers Benchmark

814 unique Pyxis analytes

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% Accuracy

Pyxis Performance

Per-Analyte Aggregation

Aggregated identification accuracy

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% Accuracy

Pyxis: 80.4% Theoretical Max: 82.3%

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MassSpecGym Benchmark

Industry-standard public dataset

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% Accuracy

Pyxis: 74.0% Theoretical Max: 78.5%

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Explore diverse chemical space

Pyxis covers an expansive range of biomolecules, with a reference library comprised of 1.8 million spectra corresponding to 99 thousand unique analytes.

Chemical Space Coverage

3D UMAP Projection • ~5,000 Representative Compounds

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Initial analysis credits for foundational models
Upload and analyze MS2 data
Molecular ID and relative quant
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Pyxis

Introducing LSM-MS2

Your Analysis Workflow in Pyxis

Core Platform Capabilities

Just upload and go

Industry-leading accuracy

Explore diverse chemical space

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