01 / DATA SYSTEM
UT-MA/26
NETWORKED MASS SPECTROMETRY DATA PLATFORM
MASCOPE
One system of record for complex spectra.
Mascope is an open-source platform for ingesting, organizing, processing and exploring high-resolution mass spectrometry data. A lightweight file agent connects instrument computers to a central server, where measurement files are stored, processed and made available through a multi-user web interface, a Python software-development kit and application programming interfaces. Current readers support Thermo Orbitrap .raw files and Tofwerk time-of-flight .h5 files. Mascope can be deployed on dedicated hardware locally or in the cloud using Docker.
MASCOPE / WEB INTERFACE
AUTOMATIC
FILE INGESTION
Transfer new acquisitions from instrument computers to the server.
CENTRALIZED
DATA + PROCESSING
Store measurement context and apply a common processing pipeline.
BROWSER + PYTHON
DATA ACCESS
Work through the web interface, Python SDK or APIs.
ANALYSIS LAYER
PEAKY + AI
Describe the analysis in plain language — deterministic chemistry code produces the figures. See it in action ↓
Current instrument-file support includes Thermo Orbitrap .raw and Tofwerk TOF .h5 files. The modular reader architecture is intended to support additional formats over time.
02 / ANALYSIS LAYER
PEAKY
AI-ASSISTED ON THE SURFACE. DETERMINISTIC UNDERNEATH.
PEAKY / CALIBRATION OUTPUT
Orbion sulfuric acid calibration using nitrate chemistry. Figure and analysis output by Peaky.
Peaky is an optional analysis layer built on top of Mascope. An analyst can describe a task in plain language or run the same workflow through a command-line interface. Peaky coordinates deterministic code for chemical-formula assignment, batch analysis, clustering, figures and reports. The language model orchestrates the workflow. It does not score isotope patterns or decide the chemistry. Mascope scoring routines and structural chemistry rules remain in the calculation path, keeping the analysis reviewable, reproducible and auditable.
Built-in reagent-aware workflows currently include bromide, uronium and nitrate CIMS chemistry. Additional reagent definitions can be configured without changing the core assignment code.
03 / ARCHITECTURE
INSTRUMENTS IN. SHARED DATA OUT.
A lightweight agent monitors the data-acquisition folder on each instrument computer and transfers each new measurement file to the Mascope server. Mascope records the file in the appropriate workspace and dated batch, applies instrument-specific signal processing and exposes the resulting data to authorized users and downstream tools. Multiple instrument computers and multiple client computers can connect to the same server simultaneously.
INSTRUMENT COMPUTERS
INSTRUMENT 01
ACQUISITION SOFTWARE + FILE AGENT
INSTRUMENT 02
ACQUISITION SOFTWARE + FILE AGENT
INSTRUMENT N
ACQUISITION SOFTWARE + FILE AGENT
MASCOPE SERVER
RAW FILE INGESTION
RELATIONAL DATABASE
SIGNAL PROCESSING
ACCESS CONTROL
WEB APPLICATION
API + SDK
LOCAL HARDWARE OR CLOUD SERVER
CLIENTS + TOOLS
WEB CLIENT 01
WEB CLIENT M
PYTHON SDK
PEAKY + DOWNSTREAM TOOLS
04 / DATA ORGANIZATION
CONTEXT PRESERVED
MORE THAN A FOLDER OF RAW FILES
High-resolution mass spectrometry campaigns produce many files across dates, samples, reagent ions, polarities and operating modes. Mascope organizes measurements in a structured hierarchy so that acquisition context remains connected to the processed data.
Why the hierarchy matters
It reduces ambiguity when measurements are revisited, compared across operating modes or accessed by researchers who did not perform the original acquisition. The same structure is available through the browser application and programmatic interfaces.
MASCOPE / DATA ORGANIZATION
A COMMON PIPELINE FOR COMPLEX SPECTRA
Mascope applies instrument-specific processing while presenting the results through a shared data model. The pipeline converts raw profile data into calibrated, quality-controlled peak information that can be explored or passed to downstream analysis tools.
Mascope provides calibrated peaks, candidate matching and match scores. Broader chemical-formula assignment and post-processing workflows can be performed through the optional Peaky analysis layer.
MASCOPE / SIGNAL PROCESSING
Instrument-specific processing
Orbitrap and time-of-flight data are handled using processing routines appropriate to their different peak shapes and resolution behaviour while remaining accessible through the same user and programming interfaces.
DOWNSTREAM ANALYSIS / OPEN SOURCE
Peaky — AI-native analysis toolbox for Mascope
Peaky adds multi-pass chemical-formula assignment, co-variation clustering and standard reporting on top of Mascope data — Van Krevelen and Kendrick views, tiered assignment tables and iterable PDF reports.
It is open source under the Apache-2.0 license and built on the Mascope SDK.
VIEW PEAKY ON GITHUB
06 / ACCESS
WEB + SDK + API
ONE DATA SYSTEM. SEVERAL WAYS TO WORK.
Self-hosting keeps the deployment environment, access policies, storage and backups under the operator’s control. Production deployment still requires appropriate infrastructure management, security, HTTPS, secrets handling and backup procedures.
07 / REFERENCE WORKFLOW
ORANGE PEELING
ONE EXPERIMENT. THE COMPLETE DATA PATH.
01 ORBION ACQUISITION → 02 AUTOMATIC FILE TRANSFER → 03 MASCOPE PROCESSING → 04 PEAKY ANALYSIS → 05 FIGURES + REPORTS
DATA OUTPUT / ORANGE PEELING
TECHNICAL PREPRINT
Networked open-source infrastructure for scalable CIMS analysis
The reference workflow demonstrates instrument-to-server transfer, centralized processing, browser and SDK access, and reproducible downstream analysis using Orbion, Mascope and Peaky.
In a reference experiment, Orbion measured compounds released during orange peeling and their subsequent oxidation products using complementary chemical-ionization modes. A file agent transferred new acquisitions to a Mascope server for online processing. Mascope produced calibrated and centroided peak information, time series and candidate-match results. Peaky then accessed the processed data for downstream formula assignment, comparison, visualization and report generation.
08 / MEASUREMENT SYSTEM
ORBION
GOLD IN GOLD OUT
Generate high-resolution multi-pressure CIMS data with Orbion.
Orbion combines complementary ion chemistry and high-resolution mass analysis. Mascope receives, processes and organizes the resulting measurement data.
09 / TECHNICAL SUMMARY
PRIMARY FUNCTION — Ingestion, organization, processing, storage and exploration of high-resolution mass spectrometry data
CURRENT INPUT FORMATS — Thermo Orbitrap .raw and Tofwerk time-of-flight .h5 files
AUTOMATIC INGESTION — Lightweight agent monitors instrument acquisition folders and transfers new measurement files to the server
DATA ORGANIZATION — Workspaces, datasets, dated batches, operating modes and samples
SIGNAL PROCESSING — Profile-spectrum summing, empirical peak modelling, signal detection, centroiding, quality control and internal mass calibration
MATCHING — Comparison of calibrated peaks with configured candidate ions or elemental compositions using mass and isotope-pattern evidence
USER INTERFACE — Multi-user browser application
PROGRAMMATIC ACCESS — Python SDK and application programming interfaces
OUTPUTS — Calibrated and centroided peak lists, time series, candidate matches and match scores
DEPLOYMENT — Self-hostable with Docker on local or cloud infrastructure
IMPLEMENTATION — Python and FastAPI backend, PostgreSQL relational database, Vue web interface and Python SDK
LICENSE — Apache License 2.0
OPTIONAL ANALYSIS LAYER — Peaky for formula assignment, batch analysis, clustering, visualization and reporting
EXTENSIBILITY — Modular instrument readers and interfaces for downstream analysis tools
MASCOPE / DEPLOYMENT
CONNECT YOUR INSTRUMENTS, DATA AND ANALYSIS.
Tell us which instruments you use, how the data are currently handled and where the analysis workflow slows down.
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