Rules to use to override SIM ions from a sequence (LC/MS)

You are able to override the SIM ions in the method by specifying the target masses in the Sequence Table. You enter the override SIM ions in the SQ:SIM Mass column.

The SIM ions that get overridden and how their mass is changed is defined  by a set of rules. You will input a string of masses into the Sequence Table using a pattern similar to "xxx;xxx;xxx" where "xxx" is replaced by masses. This input is validated by a separate set of rules. If validation passes, the Mass Overrides will be applied to the SIM ions.

• SIM ions in the original method are split by Polarity first. Then, they are sorted based on Gain values
• Each Mass Override indicates polarity by a positive number (positive polarity) or a negative number (negative polarity).
• Target masses for Mass Overrides are numbers separated by a semicolon (";").
• SIM Mass input for Mass Overrides can have one or mixed polarities (for example, "101; - 201; 301"), which need to match the polarities of the SIM ions in the original method.
• The number of target SIM ions in the Sequence Table needs to match the number of SIM ions in the original method for each Gain value in the same Polarity.
• When you have multiple Time Segments, Mass Overrides only apply to the SIM ions in the first Time Segment.
• If the method has a different number of SIM ions for multiple Gain values for the same polarity in the method, this method does not support mass override. For example, if Gain1 has 2 SIM ions in the method, then Gain2 for the same polarity should also have 2 SIM ions to support mass override.

Example 1 - simple case

Mass Overrides Input and Original Method

Mass Overrides: 101; -201

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 2	0.1	-
SIM3	1.1	+
SIM4	1.1	-
SIM5	2.2	+
SIM6	2.2	-

Split by Polarity

Positive Overrides: 101

Negative Overrides: 201

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 3	1.1	+
SIM5	2.2	+
SIM2	0.1	-
SIM4	1.1	-
SIM6	2.2	-

Apply Override

SIM Ion	Mass	Gain	Polarity
SIM 1	101	0.1	+
SIM 3	101	1.1	+
SIM5	101	2.2	+
SIM2	201	0.1	-
SIM4	201	1.1	-
SIM6	201	2.2	-

Example 2 - duplicate gain

Mass Overrides Input and Original Method

Mass Overrides: 101; -201, 301

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 2	2.2	-
SIM3	1.1	-
SIM4	0.1	+

Split by Polarity

Positive Overrides: 101; 301

Negative Overrides: 201

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 4	0.1	+
SIM 3	1.1	-
SIM 2	2.2	-

Apply Override

SIM Ion	Mass	Gain	Polarity
SIM 1	101	0.1	+
SIM 4	301	0.1	+
SIM 3	201	1.1	-
SIM 2	201	2.2	-

Example 3 - Error

Mass Overrides Input and Original Method

Mass Overrides: 101; -201, 301

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 2	2.2	-
SIM3	1.1	-
SIM4	0.1	+

Split by Polarity

Positive Overrides: 101

Negative Overrides: 201

SIM Ion	Gain	Polarity
SIM 1	0.1	+
SIM 4	0.1	+
SIM 3	1.1	-
SIM 2	2.2	-

Apply Override

The override fails because the method has two positive SIM ions with a gain of 0.1, so you need to specify two mass overrides.

The number of mass overrides must match the number of SIM ions for each unique gain in the same polarity.

See Also

Run samples

Run a sequence (LC/MS)