Vendors of Mass Spectrometers for Proteomics Research

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This page gives an overview of the different mass spectrometers by vendor. Notice that the point of view is highly biased for the kind of activities done by the Proteomics task force at BioAssist. Please consult the vendor link for more accurate description of the mass spectrometers.

Thermo (a.k.a. Thermo Finnegan)

Thermo is the main vendor for Orbitrap-LTQ and FTICR-LTQ instruments. They are usually referred to by just Orbitrap and FTICR respectively.

Orbitraps and FTICR are similar from the data analysis perspective. Orbitraps are becoming more widespread because they are cheaper than FTICR.

The Orbitraps have very high resolution at the MS level (useful for quantitation for example) and good mass accuracy. The ions selected in the Orbitrap are then fragmented in the LTQ. The LTQ scan rate is very fast although the resolution is not as high as other mass spec analyzers.

Having a fast rate for scan acquisition allows to fragment more MS ions than with a slower scan rate. Thus the dynamic range is broader with faster scans.

Orbitraps can be configured for not using the LTQ and instead fragment the ions in the same Orbitrap. This gives very high resolution at the MS/MS although the scan rate becomes much slower.

The latest Orbitraps support the use of ETD and CID fragmenation modes in the same run.

Thermo also commercializes standalone LTQ (Ion traps) which are considered nowadays to be low resolution instruments but still are used because they are very versatile and relatively cheap.

LTQs are still one of the commonest mass spectrometer found in many proteomics labs.


Bruker is pushing aggressively the performance of the newest QTOFs in order to achieve fast scan rates without losing resolution at the MS/MS level.

Having a good MS/MS resolution is important for activities like PTMs or de Novo sequencing.

The newest instruments from Bruker also support ETD fragmentation.

ABI (a.k.a. Applied Biosystems)

The most famous instruments from ABI are the QSTAR series, which are QTOFs.

Their QTRAP instruments are becoming very popular for MRM experiments.

Waters (a.k.a. Micromass)

In 1997 Waters acquired Micromass which was one of the traditional mass spectrometers vendors. The word Micromass is still used in the instrument software and in proteomics community to refer to Waters instruments.

Their high-end mass spectrometers are QTOFs.

They are also the main provider for MALDI-TOFs which are very widespread.


Agilent has a very good reputation for chromatography systems for mass spectrometers. They have recently started to provide new innovative mass spectrometers. They have a special focus on making mass spectrometers easier to operate.

See also the portal page for proteomics on this wiki.