Name: ms/ms scan modes and fragment ions
Uploaded: 2025-12-12T12:28:58.000Z
Duration: 1 min 21 s
Channel: JoVE

Tandem mass spectrometry, or MS/MS, combines two mass analyzers in sequence, connected by a collision or interaction cell.
First, the samples are ionized to generate a mixture of ions, which enters the first mass analyzer.
This analyzer separates the ions and selects only a particular ion&#8212;the precursor ion&#8212;to move into the collision cell.
The collision cell contains inert gas molecules, which collide with precursor ions, fragmenting them into product ions.
These ions are run through the second mass analyzer, where they are separated and finally detected.
MS/MS generates various spectra.
Product-ion spectra are obtained when the first analyzer selects a precursor ion and the second analyzer scans all the masses.
Precursor-ion spectra are generated by scanning through precursor ions in the first analyzer and selecting a product-ion in the second analyzer.
To obtain neutral loss spectra, both mass analyzers are scanned together, with the second analyzer offset by the mass of a selected neutral fragment.
MS/MS is used for structural elucidation and complex mixture analysis.

tandem mass spectrometry

Tandem Mass Spectrometry

Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called collision-induced dissociation (CID). Other techniques involve interaction with the surface through surface-induced dissociation (SID); interaction with low-energy electrons, called electron-capture dissociation (ECD); or through an intense laser beam, called photo-induced dissociation (PID).Tandem mass spectrometry can be used for various experiments by varying the mode of operation of the two mass analyzers. When the first mass analyzer selects a particular precursor ion and the second mass analyzer scans all the fragmented product ions, it is called a product-ion scan, and the spectra obtained by this experiment are called product-ion spectra. Alternately, when the first mass analyzer scans all the precursor ions and the second mass analyzer selects a particular product ion, it is called 'precursor-ion mode', and the spectra are termed precursor-ion spectra. Another experiment can be performed by scanning both the analyzers simultaneously with an offset of a mass equal to a neutral fragment lost by the ion to be monitored. Such a mode is called 'neutral-loss scanning mode', and the corresponding spectra are called neutral-loss spectra.The instrumentation of tandem mass spectrometry can be varied. Tandem-in-space spectrometers use two independent mass analyzers in two different regions in space, for example, a triple quadrupole mass spectrometer and TOF&#8211;TOF spectrometer. On the other hand, a tandem-in-time spectrometer, such as a quadrupole ion-trap instrument, uses the same spatial region to fragment the ions and dissociate and analyze a selected ion of interest, but at different times by expelling the unwanted ions. Tandem-in-time spectrometers can be used to perform MSn experiments. &#160;&#160;

Tandem mass spectrometry, or MS/MS, combines two mass analyzers in sequence, connected by a collision or interaction cell.
First, the samples are ionized ...

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Analytical Chemistry

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Principles of Mass Spectrometry

KEY TERMS AND CONCEPTS

ms/ms scan modes and fragment ions

Tandem mass spectrometry uses two or more mass analyzers in series to improve selectivity and lower chemical noise during analyte detection. A set of analyzers separated by an interaction cell lets the instrument break ions apart and study the fragment ions that form.

Fragmentation happens in the interaction cell and can be caused in several ways. Collision-induced dissociation, or CID, uses inert gases such as nitrogen, argon, or helium. Other methods include surface-induced dissociation (SID), electron-capture dissociation (ECD), and photo-induced dissociation (PID), which uses an intense laser beam.

Tandem mass spectrometry can also run in different scan modes. In a product-ion scan, the first mass analyzer selects one precursor ion, and the second analyzer scans the fragment product ions. The result is a product-ion spectrum. In precursor-ion mode, the first analyzer scans precursor ions, and the second selects one product ion. This gives a precursor-ion spectrum. A neutral-loss scan is different again. Both analyzers scan together with a mass offset that matches the neutral fragment lost by the ion being monitored.

The instrument design can also vary. Tandem-in-space spectrometers use two separate mass analyzers in different regions, such as a triple quadrupole mass spectrometer or a TOF-TOF spectrometer. Tandem-in-time spectrometers, such as a quadrupole ion trap, use the same space at different times to fragment and analyze a chosen ion by removing unwanted ions. These instruments can also perform MSn experiments.

MS/MS Scan Modes and Fragment Ions

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Tandem mass spectrometry uses two or more mass analyzers in series to improve selectivity and lower chemical noise during analyte detection. A set of analyzers separated by an interaction cell lets the instrument break ions apart and study the fragment ions that form. Fragmentation happens in the interaction cell and can be caused in several ways. Collision-induced dissociation, or CID, uses inert gases such as nitrogen, argon, or helium. Other methods include surface-induced dissociation...

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key terms and concepts

Learn how tandem mass spectrometry uses CID, SID, ECD, PID, and scan modes like product-ion, precursor-ion, and neutral-loss scans to analyze fragment ions.

MS/MS Scan Modes and Fragment Ions | JoVE K12

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MS/MS Scan Modes and Fragment Ions

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