Rules to override fraction collection parameters from a sequence (LC/MS)

You are able to override the fraction collection parameters in the method by specifying the compound, mass, or formula in the Sequence table using the following Override Method Parameters:

  • SQ: T1 Fraction target mass 1

  • SQ: T2 Fraction target mass 2

  • SQ: T3 Fraction target mass 3

Values in these columns should be formatted as follows:

  • mass

  • formula

  • compound name|formula (use a pipe character to separate compound name and formula)

  • compound name|mass (use a pipe character to separate compound name and mass)

  • For multiple entries, use a semi-colon to separate the values

  • Do not include spaces before or after the pipe or semi-colon separators

Each compound listed will be added to the method. The values in the sequence table will override the compound formula, monoisotopic mass, and m/z of each adduct in every Fraction collection trigger signal with the Fraction target mass column matching the override parameter Fraction target mass column identifier T1, T2, or T3.

The following should be considered when overriding fraction collection parameters in the sequence table:

  • The compound name is optional. If you do not specify a compound name for a target mass, the system will assign a default compound name when the method is run. The default compound name will have the format: TN_<mass>_FCN

  • Compounds with the same name but different masses entered in the same column or in other columns are not allowed.

  • You must enter a formula or mass.

    • If a formula is specified instead of the mass, the mass will be calculated based on the formula.

    • If only mass is entered, duplicate mass values are not allowed.

    • The mass of the ion species generated for the target mass cannot exceed the mass range of the instrument.

  • There cannot be more than 20 compounds total per sequence row across all the fraction target mass columns.

  • There cannot be more than 10 compounds in each Fraction target mass column.

  • For all Fraction target mass in the method with a Fraction trigger signals column of TN, the adduct species m/z will be calculated based on the target masses in the sequence column and the adduct species in the method.

  • If there is no Fraction target mass column in the method corresponding to the Fraction target mass column in the sequence, then an error will be indicated.

  • If the total number of SIMs in the method (both Acquisition Parameters and Fraction collection trigger signals parameters) exceeds 200 when the Method Override Fraction target mass column values are applied to the method, then an error will be indicated.

  • Once a Fraction target mass column is assigned to NOT logic in the associated method, then compounds in the Fraction target mass column cannot be in other Fraction target mass columns.

Example 1

Objective:  Set up a simple sequence override workflow where you enter a list of all the compounds in one override column. Both positive and negative adduct ions comprise the fraction collection trigger signal for each compound.  The same trigger criteria is applied to every compound.

The Fraction collection trigger signals table in the method is set up as follows:

mbfc_1.png

In the sequence table, override the fraction collection parameters as follows:

Method override column

Enter:

SQ: T1 Fraction target mass

284

or C10H9ClN4O2S

or Sulfachloropyridazine|284

or Sulfachloropyridazine|C10H9ClN4O2S

When the sequence is run, the resulting method is set up as follows:

mbfc_override_1.png

Example 2

Objective: Setup a simple Sequence override workflow where compounds with fraction collection trigger signals based on positive adduct ions are entered in one column, and compounds with fraction collection trigger signals based on negative adduct ions are entered in a second column.  Compounds in column T1 will have different fraction collection peak trigger criteria than compounds in column T2.

The Fraction collection trigger signals table in the method is set up as follows:

mbfc_2.png

In the sequence table, override the fraction collection parameters as follows:

Method override column

Enter:

SQ: T1 Fraction target mass

279

or Sulfamethazine|279

SQ: T2 Fraction target mass

309; 283; 269

or Sulfadimethoxine|309;Sulfachloropyridazine|283;Sulfamethizole|269

When the sequence is run, the resulting method is set up as follows:

mbfc_override_2.png

See Also

Run samples

Run a sequence