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INSTRUMENT SYSTEMS

How a mass spectrometer is built

LEARNING PORTAL

A mass spectrometer is a chain of subsystems working together: sample handling, vacuum, ion generation, ion transport, mass analysis, and detection, supported by control software, electronics, and laboratory infrastructure.

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This is the core of the portal. Learn this architecture and every other topic has a place to sit. 

The system map

We created this as way to hold the whole instrument in your head before you open a subsystem. Left to right is the ion path. Vacuum wraps that path. Control, electronics, and infrastructure sit under it.

When a later page mentions a turbo pump or an ion guide, this is where it lives.

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Help us build a better training resource.

If you've found an issue, have a suggestion for improvement, or would like to request additional topics, please get in touch. Every piece of feedback helps us make the portal more useful for the mass spectrometry community.

Engineering expertise when you need it

If you're looking for technical support, instrument servicing, system upgrades, or engineering consultancy, discover how Massmend can support your laboratory and equipment throughout its lifecycle.

The ion path

This is the instrument. Everything else exists so this path can happen.

A molecule is introduced, ionised, guided, separated, and measured. If you can follow that sequence, you can place every other page in this portal on a real machine.

Sample Handling

Get the sample from the bench into the source — intact, on time, and in a form the instrument can ionise.

Autosampler · LC interface · GC interface · Syringe pump · Valves · Capillaries · Transfer line · Nebulisation

Vacuum System

Create and hold the low-pressure environment ions need to survive. Without vacuum, there is no free path and no stable beam.

Chamber · Turbo pumps · Backing pumps · Ion pumps · Gauges · CF hardware · Leak detection · Bakeout

Ion Generation

Turn molecules into ions and extract them into the optics. The source sets what species you can see and how much signal you start with.

Source fundamentals · Filaments · Spray needles · HV electrodes · EI · CI · ESI · APCI · MALDI · ICP

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Introduction

Start your learning journey with an overview of the guide, what you'll learn, and how to navigate the content effectively. 

Ion Transport

Focus, guide, and hand ions to the analyser with as little loss as possible. This is where transmission is won or thrown away.

Ion optics · Lenses · Skimmers · Ion guides · Multipoles · Apertures · Differential pumping

Mass Analysis

Separate ions by mass-to-charge. Different analysers make different trade-offs in speed, resolution, mass range, and accuracy.

Quadrupoles · TOF · Orbitrap · Linear ion trap · 3D ion trap · Magnetic sector · FT-ICR · Hybrids

Detection

Turn arriving ions into a measurable signal, then get that signal out of the vacuum and into the electronics cleanly.

Electron multipliers · MCP · Faraday cups · Conversion dynodes · Preamplifiers · Shielding · Calibration

Control & Software

Run the instrument: timing, methods, acquisition, firmware, and the interface the operator actually uses.

Instrument control · Firmware · Embedded software · Data acquisition · Calibration · Method development · UI

Electrical Systems

Supply the voltages, RF, timing, and interlocks that every other subsystem depends on.

HV supplies · RF generators · Analog front-end · FPGA · Power supplies · Motion control · EMC & grounding

Infrastructure

The room around the instrument: gases, cooling, exhaust, and utilities. If this layer is wrong, the hardware never settles.

Utilities · Cooling · Nitrogen · Compressed air · Regulators · Exhaust · Environmental control · Facility requirements

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Foundations

Build a solid understanding of the scientific and engineering principles that underpin mass spectrometry.

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Instrument Systems

Take a guided tour through every major subsystem of a mass spectrometer. 

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Operation

Learn how to safely and effectively operate a mass spectrometer throughout its entire lifecycle.

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Maintenance

Keep instruments performing at their best through structured preventive maintenance and servicing.

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Troubleshooting

Develop a systematic approach to diagnosing and resolving instrument problems. 

Maintenance

Keep instruments performing at their best through structured preventive maintenance and servicing.

Operation

Learn how to safely and effectively operate a mass spectrometer throughout its entire lifecycle.

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Instrument Systems

Take a guided tour through every major subsystem of a mass spectrometer. 

Foundations

Build a solid understanding of the scientific and engineering principles that underpin mass spectrometry.

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Supporting systems

The path above only runs if vacuum, power, software, gases, and the room are right. These blocks don’t carry the beam but are essential for operation.

Learning Portal

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