The following table describes the parameters that you can specify for the activation type.

 

Parameter

Description

CID Activation Type

Assisted Collision Energy

(Available with a ddMS2 scan.)

The MS selects the optimal collision energy from those you specify. Assisted collision energy slows down the spectral acquisition rate.

Default: Deselected

CID Collision Energies (%)

(Available when the Assisted Collision Energy checkbox is selected.)

The MS selects the optimal collision energy (CE) from those you specify in the next field.

Assisted CE slows down the spectral acquisition rate. Therefore, the following is recommended:

  • Subtract 20–30 ms from the recommended Maximum Injection Time. For example, for an FTMS2 resolving power of 60,000, change the maximum injection time from 118 ms to 88 ms.

Enter 2 to 5 collision energy values as numbers, separated by commas (for example: 15, 30, 45).

Range: 0–100; default: 15,30,45

CID Collision Energy (%)

Specify the percentage of RF amplitude to fragment the ions.

Higher collision energy leads to greater energy deposition, generally producing more fragmentation.
Lower collision energy results in less energy deposition, typically yielding less fragmentation.

Range: 0–100; default: 30

CID Activation Time (ms)

Specify the amount of time to resonantly activate the precursor.

A low activation time coupled with low maximum injection time and low resolution (or fast scan rate for Ion Trap) can be used to speed up the rate of spectral acquisition. However, a higher CID collision energy may be needed to observe the same fragmentation pattern. Alternatively, some researchers have used very long activation times (100's of milliseconds) with low CID collision energy to promote high-entropy rearrangement dissociations.

Range: 0.5–1,000; default: 10

Activation Q

Specify the value of the Q parameter for CID activation. The Q parameter determines the stability of an ion’s trajectory in an Ion Trap mass analyzer.

  • A lower activation Q results in lower energy deposition, which generally leads to less fragmentation, but enables you to view fragment ions of a lower m/z value.
  • A higher activation Q results in greater energy deposition, which generally leads to more fragmentation. However, fragment ions of a lower m/z are not stable in the Ion Trap and as a result, not observed. CID collision energy will likely need to be changed to achieve best performance when Activation Q is changed.

Range: 0.05–0.8; default: 0.25

Multistage Activation

(Available with a ddMS2 scan.)

Select to perform a multistage activation to activate a precursor followed by its neutral loss species.

Default: Deselected

NOTE: Multistage activation is not data dependent. The activation of the neutral loss m/z is performed without prior detection of the species. This adds time to each scan.

Neutral Loss Mass

(Available when the Multistage Activation is enabled.)

Specify the neutral loss mass to activate in a multistage activation scan.

Range: 0–2,000; default: 50.0001

NOTE: Multistage activation is not data dependent. The activation of the neutral loss m/z is performed without prior detection of the species. This adds time to each scan.

 

HCD Activation Type

Assisted Collision Energy

(Available with a ddMS2 scan.)

The MS selects the optimal collision energy from those you specify. Assisted collision energy slows down the spectral acquisition rate.

Default: Deselected

HCD Collision Energy Type

Specify the collision energy type from the following options:

  • Normalized: Normalized collision energy allows the collision energy to be set as a percentage.
  • Absolute: Absolute collision energy allows the collision energy to be set in volts.

HCD Collision Energy/Energies (%)

(Available when HCD Collision Energy Type is set to Normalized.)

Specify the normalized accelerating voltage (as a percentage) that the MS uses to accelerate ions into the ion routing multipole (IRM), where fragmentation occurs.

Higher collision energy leads to greater energy deposition, generally producing more fragmentation.
Lower collision energy results in less energy deposition, typically yielding less fragmentation.

Enter 1 to 5 collision energy values as numbers, separated by commas (for example: 30, 31, 32, 33, 34).

Range: 0–200; default: 30

HCD Collision Energy/Energies (V)

(Available when HCD Collision Energy Type is set to Absolute.)

Specify the absolute accelerating voltage (in volts) that the MS uses to accelerate ion into the ion routing multipole (IRM), where fragmentation occurs.

Enter 1 to 5 collision energy values as numbers, separated by commas (for example: 30, 31, 32, 33, 34).

Range: 0–200; default: 30

 

UVPD Activation Type (Optional)

Use Calibrated Molecular Weight-Dependent UVPD Activation Time

Select to have the MS automatically determine the UVPD activation time based on the calibrated molecular weight.

Default: Selected

UVPD Activation Time (%)

(Available when “Use Calibrated Molecular Weight-Dependent UVPD Activation Time” is selected.)

Specify the amount of time that the precursor ion is activated by the UVPD laser in the Ion Trap.

Range: 1–1,000; default: 100

UVPD Activation Time (ms)

(Available when “Use Calibrated Molecular Weight-Dependent UVPD Activation Time” is deselected.)

Specify the amount of time that the precursor ion is activated by the UVPD laser in the Ion Trap.

Range: 0.4–4,000; default: 8

 

IRMPD Activation Type (Optional)

IRMPD Activation Q

Precursor ion Q during IRMPD.

Range: 0.05–0.8; default: 0.15

IRMPD Normalized Laser Power (%)

Specify the normalized laser power (as a percentage) used to irradiate ions during IRMPD.

Range: 1–100; default: 20

IR-TMT

Perform IRMPD using Ion Parking to maximize TMT Reporter ion yield.

When this option is enabled, the system automatically sets the “IRMPD Normalized Laser Power” and “IRMPD Activation Q” parameters to optimal values for TMT generation and hides them from view.

Default: Deselected